Contacts of the helix formed by residues 138 - 152 (chain D) in PDB entry 1Y1V
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 138 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134D THR* 3.5 25.6 - - + +
135D GLY* 4.8 1.9 - - - +
136D GLY 3.2 2.8 - - - -
137D ASN* 1.3 81.8 - - - +
139D LYS* 1.3 64.9 + - - +
140D ASP* 2.9 10.2 + - - +
141D LEU* 2.6 52.9 + - - +
142D LYS* 3.3 13.4 + - - +
35G GLU* 3.4 39.6 + - - +
36G GLY* 3.8 11.7 - - - +
46G LEU* 3.9 5.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 139 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136D GLY 4.8 0.6 + - - -
137D ASN* 3.0 10.7 + - - +
138D ASN* 1.3 75.5 - - - +
140D ASP* 1.3 92.3 + - - +
142D LYS* 3.3 16.4 + - + +
143D ASN* 3.1 44.3 + - - +
105G PRO 5.6 2.6 + - - -
107G LYS* 4.8 16.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 140 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138D ASN* 2.8 7.4 + - - +
139D LYS* 1.3 96.3 + - - +
141D LEU* 1.3 64.3 + - - +
143D ASN* 3.6 3.7 + - - +
144D THR* 2.8 28.3 + - - -
36G GLY* 3.8 24.5 - - - +
37G SER 5.4 0.3 - - - +
44G TYR* 3.6 27.3 - - + -
46G LEU* 4.3 9.9 - - + -
105G PRO* 3.7 20.2 - - + +
155G SER 5.3 4.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 141 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59D ILE* 4.3 11.9 - - + -
63D LEU* 4.8 8.7 - - + -
130D LEU* 4.2 16.2 - - + -
134D THR* 4.2 18.6 - - + +
138D ASN* 2.6 34.9 + - + +
140D ASP* 1.3 72.5 - - - +
142D LYS* 1.3 68.3 + - + +
144D THR* 3.1 14.2 - - + -
145D MET* 2.9 39.5 + - + +
35G GLU* 4.9 5.2 - - - +
46G LEU* 3.7 31.4 - - + +
47G CYS* 4.6 8.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 142 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127D ASP* 5.6 5.6 - - - +
130D LEU* 4.0 29.6 - - + -
131D GLU* 6.0 6.1 - - - +
134D THR* 6.1 4.5 - - + -
136D GLY* 3.9 24.7 + - - -
138D ASN 3.3 8.7 + - - +
139D LYS* 3.3 16.4 + - + +
140D ASP 3.2 0.6 - - - -
141D LEU* 1.3 76.2 - - + +
143D ASN* 1.3 59.4 + - - +
145D MET* 2.6 28.8 + - - +
146D GLN* 3.2 13.5 + - + +
----------------------------------------------------------
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 LYS* 3.1 42.4 + - - +
140D ASP* 4.0 5.3 + - - +
142D LYS* 1.3 80.1 - - - +
144D THR* 1.3 60.3 + - - +
146D GLN* 3.4 19.4 + - - +
147D TYR* 3.1 24.3 + - - +
102G GLN* 3.3 32.0 + - - +
104G GLY 5.0 1.3 - - - -
105G PRO* 4.7 8.8 + - + -
107G LYS* 6.0 1.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 144 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59D ILE* 4.5 2.0 - - + -
140D ASP 2.8 17.4 + - - -
141D LEU* 3.1 13.4 + - + +
142D LYS 2.7 3.6 + - - -
143D ASN* 1.3 72.5 - - - +
145D MET* 1.3 59.9 - - - +
147D TYR* 3.4 4.3 + - - +
148D LEU* 2.6 51.3 + - + +
2G PHE* 4.0 18.8 - - + -
46G LEU* 3.4 27.4 - - + +
104G GLY* 4.6 0.4 - - - -
105G PRO* 3.0 28.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 145 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56D ARG* 4.3 20.9 - - + +
59D ILE* 4.0 24.7 - - + -
60D LYS* 4.9 6.1 - - + +
126D ILE* 4.2 36.8 - - + -
130D LEU* 4.2 17.9 - - + -
141D LEU* 2.9 36.9 + - + +
142D LYS* 2.6 15.0 + - - +
144D THR* 1.3 70.2 - - - +
146D GLN* 1.3 55.0 + - + +
148D LEU* 3.6 15.4 - - + +
149D THR* 2.6 37.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 146 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123D LEU* 4.5 17.9 - - + +
127D ASP* 5.6 8.9 + - - +
142D LYS* 3.2 11.6 + - - +
143D ASN* 3.7 19.6 - - - +
144D THR 3.2 0.2 - - - -
145D MET* 1.3 73.5 - - + +
147D TYR* 1.3 55.5 + - - +
149D THR* 2.6 16.4 + - - +
150D ASN* 2.5 47.9 + - - +
102G GLN* 6.0 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 147 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52D LEU* 3.4 38.4 - - + +
143D ASN 3.1 14.5 + - - +
144D THR 3.6 2.9 - - - +
146D GLN* 1.3 77.6 - - - +
148D LEU* 1.3 61.2 + - - +
150D ASN* 4.5 0.2 - - - -
151D PHE* 2.7 72.5 + + - +
2G PHE* 4.8 8.5 - + - -
87G VAL* 4.4 3.8 - - - +
88G ASP* 2.6 40.1 + - - -
89G GLY* 3.7 2.5 - - - -
102G GLN* 3.9 7.9 - - - +
103G VAL* 2.9 28.4 - - + +
104G GLY* 3.2 31.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 148 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52D LEU* 3.9 13.2 - - + -
53D SER 3.3 22.2 - - - +
55D ALA* 3.9 8.3 - - + -
56D ARG* 3.2 44.7 - - + +
59D ILE* 3.4 33.0 - - + -
144D THR* 2.6 31.6 + - + +
145D MET* 3.8 10.5 - - - +
147D TYR* 1.3 79.0 - - - +
149D THR* 1.3 50.6 + - - +
152D SER* 2.5 36.0 + - - +
2G PHE* 4.5 10.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 149 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56D ARG* 3.5 8.3 - - - +
119D ARG* 5.2 9.5 - - - +
122D GLU* 2.6 33.6 + - + +
123D LEU* 3.3 40.4 - - + +
126D ILE* 3.6 11.0 - - + +
145D MET 2.6 16.4 + - - +
146D GLN 2.6 13.5 + - - +
148D LEU* 1.3 72.3 - - - +
150D ASN* 1.3 63.4 + - - +
152D SER* 3.5 9.0 + - - -
221D TYR* 4.0 8.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 150 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119D ARG* 4.9 14.0 - - - +
123D LEU* 3.7 28.0 - - - +
146D GLN* 2.5 33.2 + - - +
147D TYR 3.8 2.0 - - - +
149D THR* 1.3 79.1 - - - +
151D PHE* 1.3 72.0 + - + +
152D SER* 3.5 1.0 - - - +
221D TYR* 3.9 16.5 + - - -
142G ARG* 3.4 36.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 151 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52D LEU* 4.1 24.5 - - + +
147D TYR* 2.7 60.6 + + + +
150D ASN* 1.3 80.4 - - + +
152D SER* 1.3 70.9 + - - +
153D ARG* 4.4 5.4 - - - +
182D SER 5.7 0.3 - - - +
88G ASP* 4.2 20.0 - - + +
89G GLY* 3.5 28.3 - - - -
90G THR* 3.2 27.8 - - - -
142G ARG* 3.7 35.7 - - + +
171G ILE* 5.7 2.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 152 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52D LEU* 4.3 6.0 - - - +
53D SER* 3.1 30.5 - - - +
56D ARG* 3.5 14.1 + - - -
148D LEU 2.5 24.3 + - - -
149D THR 3.5 14.2 + - - -
150D ASN 3.5 0.9 - - - +
151D PHE* 1.3 88.8 - - - +
153D ARG* 1.3 64.4 + - - +
154D PHE 4.5 2.0 - - - -
221D TYR* 4.2 17.4 + - - -
----------------------------------------------------------
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