Contacts of the helix formed by residues 131 - 145 (chain D) in PDB entry 4UN7
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 131 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129D ASN* 3.0 17.3 + - - +
130D LYS* 1.3 75.7 - - - +
132D LYS* 1.3 62.8 + - - +
133D ALA* 3.2 12.6 + - - +
134D LEU* 3.2 40.0 + - + +
135D LEU* 3.3 16.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 132 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130D LYS 3.5 4.6 + - - -
131D ASN* 1.3 71.5 + - - +
133D ALA* 1.3 59.4 + - - +
135D LEU* 3.2 8.1 + - - +
136D GLU* 2.9 59.8 + - + +
151D ILE* 4.7 10.1 - - + -
161D TYR* 3.6 51.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 133 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99D ARG* 5.3 10.3 - - - +
131D ASN* 3.2 9.3 + - - +
132D LYS* 1.3 79.2 - - - +
134D LEU* 1.3 57.4 + - - +
136D GLU* 3.5 15.4 - - - +
137D ILE* 3.1 34.4 + - + +
140D ARG* 4.9 1.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 134 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19D ILE* 4.1 20.0 - - + -
95D LEU* 5.3 6.5 - - + -
98D ILE* 4.1 15.5 - - + -
109D PHE* 4.0 23.6 - - + -
113D LEU* 4.4 15.7 - - + -
129D ASN* 4.1 29.8 - - + +
131D ASN* 3.2 28.0 + - + +
132D LYS 3.1 0.4 - - - -
133D ALA* 1.3 76.2 - - - +
135D LEU* 1.3 61.8 + - + +
137D ILE* 3.4 13.3 + - + +
138D VAL* 2.9 36.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 135 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113D LEU* 4.9 9.6 - - + -
127D ILE* 4.3 24.7 - - + +
129D ASN* 3.8 30.5 - - + +
131D ASN 3.3 10.3 + - - +
132D LYS* 3.2 7.5 + - - +
134D LEU* 1.3 78.5 - - + +
136D GLU* 1.3 50.8 - - - +
138D VAL* 3.0 5.4 + - + -
139D SER* 2.5 37.1 + - - -
151D ILE* 3.7 16.6 - - + -
161D TYR* 3.8 38.8 - - + +
162D VAL 4.1 3.1 - - - +
163D LEU* 3.4 23.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 136 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132D LYS* 2.9 53.3 + - + +
133D ALA* 3.5 14.9 - - - +
134D LEU 3.2 0.2 - - - -
135D LEU* 1.3 72.7 - - - +
137D ILE* 1.3 59.7 + - - +
139D SER* 3.1 4.0 + - - -
140D ARG* 2.9 49.3 + - + +
151D ILE* 3.5 20.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 137 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98D ILE* 4.3 19.3 - - + -
99D ARG* 3.9 43.7 - - + +
133D ALA* 3.1 19.2 + - + +
134D LEU* 3.5 13.0 - - + +
135D LEU 3.4 0.2 - - - -
136D GLU* 1.3 76.3 - - - +
138D VAL* 1.3 65.9 + - + +
140D ARG* 3.2 28.4 + - - +
141D TRP* 3.2 56.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 138 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109D PHE* 4.1 20.4 - - + -
110D ILE* 4.0 23.8 - - + -
113D LEU* 4.0 24.0 - - + -
127D ILE* 4.7 13.2 - - + -
134D LEU* 2.9 21.8 + - + +
135D LEU* 3.5 9.9 - - + +
137D ILE* 1.3 76.0 - - + +
139D SER* 1.3 63.3 + - - +
141D TRP* 3.2 14.5 + - + +
142D LEU* 3.0 29.6 + - + +
163D LEU* 4.2 12.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 139 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135D LEU 2.5 20.5 + - - -
136D GLU* 3.2 12.6 - - - -
138D VAL* 1.3 74.6 - - - +
140D ARG* 1.3 56.9 + - - +
142D LEU* 3.4 0.6 + - - -
143D ASN* 3.0 36.1 + - - -
149D ASN* 2.5 33.2 + - - +
151D ILE* 3.9 11.0 - - - +
163D LEU* 3.7 8.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 140 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99D ARG* 4.7 12.4 - - - +
133D ALA 4.9 0.6 + - - -
136D GLU* 2.9 32.3 + - + +
137D ILE* 3.2 33.3 + - - +
139D SER* 1.3 74.6 - - - +
141D TRP* 1.3 70.2 + - + +
143D ASN* 3.5 9.3 + - - +
144D ASN* 3.2 22.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 141 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98D ILE* 3.4 34.1 - - + -
99D ARG* 4.7 8.3 + - - +
101D PHE* 3.7 23.3 + + + -
106D GLN* 3.2 63.9 - - + +
109D PHE* 3.7 24.5 - + + -
110D ILE* 4.1 16.6 - - + -
137D ILE* 3.2 32.8 + - + +
138D VAL* 3.6 12.6 - - + +
140D ARG* 1.3 81.0 - - + +
142D LEU* 1.3 58.8 + - - +
144D ASN* 3.5 7.8 + - - +
145D LEU* 3.1 34.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 142 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110D ILE* 3.6 17.7 - - + -
127D ILE* 5.4 1.1 - - + -
138D VAL* 3.0 24.9 + - + +
140D ARG 3.3 0.2 - - - -
141D TRP* 1.3 75.1 - - - +
143D ASN* 1.3 63.1 + - - +
145D LEU* 3.1 9.3 + - + -
146D GLY 3.2 0.2 + - - -
147D VAL* 2.8 35.3 + - + +
149D ASN* 3.5 15.9 - - - +
163D LEU* 3.7 34.3 - - + -
165D ILE* 4.0 16.8 - - + -
173D PHE* 4.0 13.0 - - + -
177D ILE* 3.5 31.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 143 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139D SER* 3.0 29.8 + - - +
140D ARG* 3.8 8.4 - - - +
141D TRP 3.3 0.4 - - - -
142D LEU* 1.3 75.7 - - - +
144D ASN* 1.3 54.5 + - - +
146D GLY* 2.8 25.8 + - - -
147D VAL 3.7 12.2 - - - +
148D ARG* 4.2 10.9 - - - +
149D ASN* 3.8 12.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 144 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103D MET* 6.4 0.4 - - - +
106D GLN* 4.9 11.7 + - - +
140D ARG 3.2 14.2 + - - +
141D TRP* 3.8 6.4 - - - +
142D LEU 3.4 0.2 - - - -
143D ASN* 1.3 78.4 - - - +
145D LEU* 1.3 62.8 + - - +
146D GLY* 3.2 3.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 145 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103D MET* 3.6 38.4 - - + -
106D GLN* 5.4 6.5 - - + +
107D ILE* 4.1 19.1 - - + +
110D ILE* 4.7 9.0 - - + -
141D TRP* 3.1 23.3 + - + +
142D LEU* 3.6 7.2 - - - +
143D ASN 3.0 1.8 - - - -
144D ASN* 1.3 82.9 - - - +
146D GLY* 1.3 61.9 + - - +
147D VAL* 3.4 7.3 + - + +
172D LYS* 3.4 18.4 + - - +
176D THR* 5.3 10.7 - - + +
177D ILE* 3.7 26.7 - - + -
----------------------------------------------------------
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