Contacts of the helix formed by residues 129 - 154 (chain a) in PDB entry 4N3E
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ASN 129 (chain a).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93a ARG* 2.8 40.0 + - - +
95a ASN* 2.4 35.4 - - - +
96a ILE* 3.3 11.5 - - - +
128a VAL* 1.3 65.8 - - - +
130a GLU* 1.3 54.5 + - - +
131a GLU* 2.8 9.1 + - + +
132a GLU* 2.6 42.3 + - - +
133a VAL* 3.3 8.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 130 (chain a).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4a TYR* 3.0 37.8 + - + +
128a VAL 3.3 6.5 + - - +
129a ASN* 1.3 70.6 - - - +
131a GLU* 1.3 60.0 + - - +
133a VAL* 3.7 8.3 + - - +
134a LYS* 3.3 52.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 131 (chain a).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93a ARG* 2.2 44.6 + - - +
129a ASN* 4.3 5.4 - - + +
130a GLU* 1.3 75.2 - - - +
132a GLU* 1.3 66.6 + - - +
133a VAL 2.7 3.5 + - - -
134a LYS* 2.8 18.1 + - - +
135a ILE* 3.1 24.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 132 (chain a).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86a LEU* 5.7 0.7 - - - +
91a VAL* 3.3 12.1 - - - +
92a LEU* 2.4 40.1 - - - +
93a ARG* 2.8 24.9 + - - +
96a ILE* 3.8 18.3 - - + +
99a VAL* 4.5 1.7 - - - +
120a TYR* 3.5 28.7 + - + -
129a ASN* 2.6 36.0 + - - +
131a GLU* 1.3 73.6 - - - +
133a VAL* 1.3 55.7 + - + +
135a ILE* 3.8 8.2 - - - +
136a GLY* 3.1 22.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 133 (chain a).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4a TYR* 4.0 29.4 - - + -
6a ILE* 3.5 36.3 - - + -
120a TYR* 3.6 33.2 - - + -
128a VAL* 4.9 1.6 - - + -
129a ASN 3.9 11.0 - - - +
130a GLU* 3.7 11.0 - - + +
131a GLU 2.7 5.1 + - - -
132a GLU* 1.3 72.6 - - + +
134a LYS* 1.3 69.3 + - + +
136a GLY 3.1 10.9 + - - -
137a GLU* 3.2 19.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 134 (chain a).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130a GLU* 3.3 43.9 + - + +
131a GLU* 2.8 13.1 + - - +
133a VAL* 1.3 78.4 - - + +
135a ILE* 1.3 54.2 + - - +
137a GLU* 4.3 3.1 - - - +
138a LYS* 3.0 30.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 135 (chain a).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91a VAL* 6.4 1.6 - - + -
93a ARG* 3.7 28.7 - - - +
131a GLU* 3.1 28.7 + - + +
132a GLU* 3.8 9.0 - - - +
134a LYS* 1.3 72.4 - - - +
136a GLY* 1.3 60.3 + - - +
137a GLU 3.0 4.9 - - - -
138a LYS* 3.3 8.2 + - + +
139a LYS* 3.0 51.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 136 (chain a).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101a TYR* 4.9 9.5 + - - -
120a TYR* 3.7 12.8 - - - -
132a GLU 3.1 6.8 + - - -
133a VAL 3.1 5.1 + - - -
135a ILE* 1.3 81.7 - - - +
137a GLU* 1.3 67.5 + - - +
139a LYS* 4.2 6.0 - - - +
140a ALA* 3.5 21.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 137 (chain a).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6a ILE* 3.3 29.8 - - + -
8a LYS* 2.7 42.1 + - - +
101a TYR* 4.6 4.4 - - - -
118a VAL* 3.1 23.3 - - - +
120a TYR* 2.5 22.4 + - - +
133a VAL* 3.2 19.1 - - + +
134a LYS* 4.3 3.1 - - - +
136a GLY* 1.3 87.3 - - - +
138a LYS* 1.3 63.0 + - - +
139a LYS 3.4 0.2 - - - -
140a ALA* 4.2 2.8 - - - +
141a TYR* 3.4 22.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 138 (chain a).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134a LYS 3.0 21.4 + - - +
135a ILE* 3.7 7.4 - - + +
137a GLU* 1.3 76.0 - - - +
139a LYS* 1.3 101.2 + - - +
141a TYR* 3.8 3.8 - - - +
142a GLU* 2.8 55.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 139 (chain a).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35a GLN* 5.0 2.5 + - - +
135a ILE* 3.0 36.7 + - + +
136a GLY* 4.6 5.2 - - - +
138a LYS* 1.3 113.8 - - - +
140a ALA* 1.3 60.8 + - - +
142a GLU* 3.7 13.6 + - - +
143a PHE* 3.3 23.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 140 (chain a).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8a LYS* 4.5 3.1 - - - +
27a ARG* 3.8 26.1 + - - +
101a TYR* 5.6 4.0 - - + -
136a GLY 3.5 19.5 + - - +
137a GLU* 4.3 3.8 - - - +
138a LYS 3.4 0.2 - - - -
139a LYS* 1.3 76.6 - - - +
141a TYR* 1.3 59.0 + - - +
143a PHE* 3.9 6.9 + - - +
144a TYR* 3.2 25.8 + - - +
201a 2AN 3.8 26.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 141 (chain a).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8a LYS* 6.0 2.7 - - + -
10a GLU* 3.8 26.7 + - + -
137a GLU 3.4 18.6 + - - +
138a LYS* 3.8 5.4 - - - +
139a LYS 3.3 0.4 - - - -
140a ALA* 1.3 78.0 - - - +
142a GLU* 1.3 62.1 + - + +
144a TYR* 3.3 34.4 + + - +
145a LYS* 2.9 50.4 + - + +
201a 2AN 3.9 13.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 142 (chain a).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35a GLN* 5.0 6.0 + - - +
138a LYS* 2.8 52.9 + - + +
139a LYS* 3.7 16.6 - - - +
141a TYR* 1.3 74.9 - - + +
143a PHE* 1.3 68.7 + - - +
145a LYS* 3.1 8.4 + - - +
146a GLN* 2.9 34.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 143 (chain a).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22a ALA 5.2 0.4 - - - -
23a LEU* 3.8 16.8 - - + -
27a ARG* 3.8 41.5 - - + -
30a VAL* 3.6 36.8 - - + -
31a LEU* 3.8 35.0 - - + -
34a ALA* 3.9 13.5 - - + -
35a GLN* 3.9 12.3 - - - +
139a LYS 3.3 14.3 + - - +
140a ALA* 4.1 3.1 - - - +
141a TYR 3.4 0.2 - - - -
142a GLU* 1.3 79.2 - - - +
144a TYR* 1.3 63.4 + - - +
146a GLN* 3.2 11.8 + - - +
147a VAL* 3.1 41.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 144 (chain a).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10a GLU* 3.4 14.8 + - + -
11a GLU 3.7 3.5 + - - -
12a SER* 4.2 3.1 - - - -
19a LEU* 4.6 2.7 - - + -
23a LEU* 3.6 30.1 - - + -
27a ARG* 6.2 0.2 - - - +
140a ALA 3.2 11.7 + - - +
141a TYR* 3.3 40.8 - + - +
142a GLU 3.1 0.8 - - - -
143a PHE* 1.3 77.8 - - - +
145a LYS* 1.3 77.8 + - + +
147a VAL* 3.1 2.1 + - - +
148a GLU* 2.9 58.7 + - + +
201a 2AN 3.0 65.8 - + + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 145 (chain a).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141a TYR* 2.9 38.7 + - + +
142a GLU* 3.1 10.3 + - - +
144a TYR* 1.3 100.1 + - + +
146a GLN* 1.3 60.4 + - - +
148a GLU* 2.5 31.8 + - - +
149a GLU* 3.3 23.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 146 (chain a).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34a ALA* 3.2 29.7 + - + +
35a GLN* 3.1 37.4 + - - +
37a HIS* 5.7 3.2 - - - -
142a GLU* 2.9 18.4 + - - +
143a PHE* 3.3 13.1 - - - +
144a TYR 3.2 0.2 - - - -
145a LYS* 1.3 75.1 - - - +
147a VAL* 1.3 62.9 + - + +
149a GLU* 3.7 7.8 + - - +
150a TYR* 3.1 25.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 147 (chain a).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19a LEU* 5.4 0.7 - - + -
22a ALA* 3.8 22.0 - - + -
23a LEU* 4.1 10.3 - - + -
30a VAL* 3.8 13.0 - - + -
34a ALA* 4.6 6.1 - - + -
143a PHE* 3.2 43.7 - - + +
144a TYR 3.1 4.0 + - - +
146a GLN* 1.3 79.8 - - + +
148a GLU* 1.3 56.8 + - - +
150a TYR* 4.0 10.8 - - + -
151a LEU* 2.6 55.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 148 (chain a).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11a GLU 4.3 0.5 - - - +
12a SER* 2.5 32.1 + - - +
13a PRO* 3.5 21.1 - - + +
14a ILE* 3.5 19.5 - - + +
19a LEU* 5.0 4.2 - - + +
144a TYR* 2.9 41.8 + - + +
145a LYS* 2.5 37.9 + - - +
147a VAL* 1.3 78.1 - - - +
149a GLU* 1.3 60.8 + - - +
151a LEU* 3.5 0.4 + - - -
152a ALA* 3.2 21.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 149 (chain a).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145a LYS 3.3 15.6 + - - +
146a GLN* 3.8 7.3 - - - +
147a VAL 3.2 0.2 - - - -
148a GLU* 1.3 79.1 + - - +
150a TYR* 1.3 84.1 + - - +
152a ALA* 3.5 6.1 + - - +
153a ALA* 3.1 31.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 150 (chain a).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146a GLN 3.1 16.5 + - - +
147a VAL* 3.1 12.1 + - + +
149a GLU* 1.3 88.8 + - - +
151a LEU* 1.3 66.1 + - + +
153a ALA* 3.4 1.9 + - + -
154a ASN* 3.0 56.6 + - - +
157a VAL* 4.5 26.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 151 (chain a).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14a ILE* 3.3 37.9 - - + -
18a ARG* 3.1 46.4 + - + +
19a LEU* 3.9 18.6 - - + -
22a ALA* 4.5 1.3 - - + -
147a VAL* 2.6 40.8 + - + +
150a TYR* 1.3 79.9 - - + +
152a ALA* 1.3 60.3 + - - +
154a ASN 3.0 21.8 - - - +
155a PRO* 3.8 0.7 - - - +
157a VAL* 4.2 23.1 - - + +
158a PHE* 4.5 10.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 152 (chain a).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13a PRO* 5.9 5.4 - - + -
14a ILE* 3.5 11.8 - - + +
18a ARG* 4.9 1.1 - - - +
148a GLU 3.2 15.2 + - - +
149a GLU* 3.7 5.8 - - - +
151a LEU* 1.3 81.1 - - - +
153a ALA* 1.3 58.9 - - - +
154a ASN 3.6 0.3 + - - -
155a PRO* 4.2 13.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 153 (chain a).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149a GLU* 3.1 30.8 + - - +
150a TYR* 3.4 2.2 + - + +
152a ALA* 1.3 76.5 - - - +
154a ASN* 1.3 69.8 + - - +
155a PRO* 3.8 6.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 154 (chain a).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18a ARG* 2.9 17.7 + - - -
150a TYR* 3.0 46.7 + - + +
151a LEU* 3.0 4.2 - - - +
153a ALA* 1.3 87.1 + - - +
155a PRO* 1.3 63.8 - - - +
156a GLU* 3.2 20.8 + - - +
157a VAL* 3.5 23.8 + - + +
----------------------------------------------------------
Back to top of page
A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il