Contacts of the strand formed by residues 91 - 100 (chain B) in PDB entry 1DVM
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 ILE 91 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82B LEU 4.1 9.4 - - - +
83B MET* 3.7 36.8 - - + +
86B TRP* 4.9 4.7 - - + -
87B ASN* 2.9 44.6 + - + +
89B ASP* 4.4 5.5 - - - +
90B GLU* 1.3 79.1 + - - +
92B SER* 1.3 72.8 + - - +
93B THR* 3.8 10.3 - - + -
145B LYS* 5.6 0.2 - - - +
169B LEU* 4.6 0.9 - - + -
170B TYR* 3.1 17.3 - - - +
171B PHE* 4.1 9.0 - - + -
233B LEU* 5.9 2.9 - - + -
371B LEU* 5.8 8.1 - - + -
372B PHE* 3.2 37.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 92 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83B MET* 5.1 2.7 - - - -
91B ILE* 1.3 79.4 + - - +
93B THR* 1.3 60.9 + - - +
143B HIS 4.4 2.7 + - - -
144B THR* 3.8 23.0 + - - +
145B LYS* 3.5 31.4 - - - +
147B MET* 5.5 0.3 - - - +
169B LEU* 2.8 6.8 - - - +
170B TYR* 2.6 48.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 93 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B TYR* 5.0 9.9 - - + -
79B TYR* 3.7 30.7 + - - -
83B MET* 3.4 31.5 - - + +
91B ILE* 3.8 7.6 - - + -
92B SER* 1.3 79.5 - - - +
94B THR* 1.3 65.6 + - - +
95B ASP* 4.7 5.2 + - - -
143B HIS* 3.7 11.2 + - - +
144B THR* 5.0 0.4 - - - -
167B ASN* 5.6 1.6 - - - -
168B ALA 3.3 6.1 - - - -
169B LEU* 3.8 25.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 94 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93B THR* 1.3 78.3 - - - +
95B ASP* 1.3 68.3 + - - +
139B TRP* 2.8 37.6 + - + +
140B VAL* 4.2 11.7 - - + -
143B HIS* 3.3 26.5 - - + +
144B THR* 4.6 2.9 - - + -
166B VAL* 5.3 2.7 - - + -
167B ASN* 3.2 8.0 + - - -
168B ALA* 2.7 51.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 95 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B GLY* 5.0 0.2 - - - -
41B SER* 3.9 22.9 + - - -
42B VAL* 3.3 20.5 - - + +
45B MET* 4.0 26.8 - - + +
79B TYR* 5.4 6.1 - - - -
93B THR* 4.7 6.7 + - - -
94B THR* 1.3 84.0 + - - +
96B ALA* 1.3 63.6 + - - +
122B LYS* 4.5 5.2 + - - -
139B TRP* 3.9 6.6 + - - -
166B VAL 3.4 5.2 - - - -
167B ASN* 2.9 26.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 96 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42B VAL* 4.6 0.8 - - - +
95B ASP* 1.3 77.4 - - - +
97B ILE* 1.3 65.1 + - - +
98B PHE* 3.4 28.7 - - + -
122B LYS* 4.8 6.5 - - + +
139B TRP* 3.7 24.5 - - + +
164B VAL 4.0 0.3 - - - +
165B LEU* 3.5 2.9 - - - +
166B VAL* 2.7 49.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 97 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42B VAL* 4.7 5.8 - - + +
45B MET* 4.1 31.4 - - + +
46B LEU* 4.3 25.8 - - + +
49B THR* 4.7 6.5 - - + -
96B ALA* 1.3 78.7 - - - +
98B PHE* 1.3 58.5 + - - +
113B PHE* 4.1 17.5 - - + -
121B VAL* 3.1 24.2 - - + +
122B LYS* 2.7 36.1 + - - +
163B LEU* 3.7 25.6 - - + -
164B VAL 3.4 6.1 - - - +
165B LEU* 4.8 11.4 - - + -
309B LEU* 5.9 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 98 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96B ALA* 3.4 30.7 - - + -
97B ILE* 1.3 74.2 - - - +
99B VAL* 1.3 61.9 + - - +
122B LYS* 3.1 28.5 - - + -
124B VAL* 3.4 27.8 - - + -
126B PHE* 4.7 0.9 - - - -
135B ILE* 3.8 21.5 - - + -
136B ILE* 3.8 43.5 - - + -
139B TRP* 4.1 16.8 - + + -
140B VAL* 6.1 0.2 - - + -
162B ARG 4.4 0.2 - - - -
163B LEU* 3.3 8.2 - - - +
164B VAL* 2.7 60.0 + - + +
166B VAL* 4.8 3.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 99 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98B PHE* 1.3 75.4 - - - +
100B GLN* 1.3 72.4 + - - +
101B ARG 3.1 0.2 + - - -
103B LEU* 3.7 20.6 - - + -
105B LEU* 4.6 5.4 - - + -
121B VAL* 4.6 15.7 - - + -
122B LYS 2.8 13.3 + - - +
123B GLN* 3.3 22.9 - - + +
124B VAL 3.0 21.6 + - - -
126B PHE* 4.0 2.5 - - - -
162B ARG 3.1 12.6 - - - +
163B LEU* 4.1 11.0 - - + -
309B LEU* 4.0 24.5 - - + -
315B LEU* 4.2 5.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 100 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99B VAL* 1.3 71.6 - - - +
101B ARG* 1.3 65.2 + - - +
102B ASP* 3.1 14.5 + - + +
103B LEU* 3.2 42.4 - - + +
123B GLN* 3.9 4.2 + - - -
124B VAL 3.4 4.0 - - - -
125B ASP* 2.9 28.9 - - - +
126B PHE* 3.1 41.4 + - - +
127B SER* 4.5 1.9 + - - -
159B GLN 4.8 2.2 + - - -
161B THR 3.4 6.1 + - - -
162B ARG* 2.9 35.0 + - - +
----------------------------------------------------------
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