Contacts of the strand formed by residues 90 - 100 (chain B) in PDB entry 1VHA
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 TYR 90 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
0B SER* 3.5 22.1 + - - -
1B LEU 4.5 4.9 - - - -
3B ARG* 3.3 39.5 + - + +
53B ALA* 4.6 6.5 - - + -
82B PHE* 4.5 0.9 - - - -
85B VAL* 3.0 36.1 + - + +
86B GLN* 3.6 25.1 + - - +
88B LYS* 4.1 34.5 - - + -
89B GLY* 1.3 80.3 - - - +
91B LYS* 1.3 61.4 + - - +
155B LEU* 3.9 18.8 - - + -
156B ILE 3.5 19.5 - - - +
157B ARG* 3.8 24.8 + - - -
158B GLN* 4.3 6.0 - - - +
126C GLU* 4.7 2.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 91 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82B PHE* 4.3 13.7 - - + -
90B TYR* 1.3 72.0 - - - +
92B ILE* 1.3 76.2 + - - +
127B GLN* 5.4 2.4 - - - +
155B LEU* 3.6 9.0 - - - +
156B ILE* 3.0 60.7 + - + +
157B ARG 4.8 6.5 - - - -
158B GLN* 3.2 32.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 92 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49B ILE* 4.6 5.6 - - + -
82B PHE* 3.3 36.4 - - + -
91B LYS* 1.3 90.3 + - - +
93B GLY* 1.3 64.0 + - - +
94B ASN* 3.4 23.6 - - - +
95B VAL* 4.4 10.8 - - + +
121B LEU* 3.8 31.4 + - + +
123B CYS* 4.1 24.2 - - + +
127B GLN* 2.8 27.8 + - + +
154B LEU 4.2 1.8 - - - +
155B LEU* 4.2 16.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 93 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
0A SER* 4.1 9.1 + - - -
2A ILE 5.6 1.8 - - - -
91B LYS 3.6 2.8 + - - -
92B ILE* 1.3 71.5 - - - +
94B ASN* 1.3 67.3 + - - +
127B GLN* 2.9 24.7 + - - +
154B LEU* 2.8 19.7 + - - -
155B LEU* 4.2 0.6 - - - +
156B ILE* 3.6 31.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 94 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A ARG* 3.5 33.1 - - - +
4A ILE* 3.0 47.8 + - - +
51A GLY 4.5 1.4 + - - -
52A ALA* 3.7 15.6 + - - +
92B ILE* 3.4 4.4 - - - +
93B GLY* 1.3 80.4 - - - +
95B VAL* 1.3 74.8 + - - +
127B GLN 3.2 14.1 - - - +
153B ALA* 3.8 0.2 - - - -
154B LEU* 3.0 32.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 95 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A ILE* 5.3 0.4 - - - -
45B LEU* 3.7 22.7 - - + -
49B ILE* 4.6 1.3 - - + -
92B ILE* 4.4 13.5 - - + -
94B ASN* 1.3 86.5 + - - +
96B ASP* 1.3 60.5 + - - +
97B ILE* 3.8 14.1 - - + -
117B ILE* 4.7 1.8 - - + -
121B LEU* 4.3 17.9 - - + -
127B GLN 2.9 16.2 + - - +
128B VAL* 4.1 22.0 - - + -
129B ASN* 3.1 24.1 + - - +
152B VAL 3.5 6.1 - - - +
153B ALA* 3.8 20.2 - - + -
154B LEU 4.9 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 96 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A ILE 4.1 9.6 - - - +
5A GLY* 3.3 1.2 - - - -
6A HIS* 2.8 27.3 + - - +
51A GLY* 3.3 24.5 - - - +
95B VAL* 1.3 75.0 - - - +
97B ILE* 1.3 63.3 + - - +
129B ASN* 2.9 19.4 + - - -
131B LYS* 2.8 28.0 + - - -
150B GLU 4.2 0.2 - - - +
151B ALA* 3.4 3.6 - - - -
152B VAL* 3.1 45.6 + - + +
----------------------------------------------------------
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
----------------------------------------------------------
41B ALA* 4.1 17.0 - - + +
45B LEU* 3.7 37.5 - - + -
95B VAL* 3.8 9.2 - - + -
96B ASP* 1.3 86.4 + - - +
98B THR* 1.3 66.6 + - - +
99B ILE* 4.4 3.6 - - + -
113B MSE 5.2 0.2 - - + -
117B ILE* 5.1 5.8 - - + -
128B VAL* 5.2 0.2 - - + -
129B ASN 2.8 21.3 + - - +
130B VAL* 3.5 23.5 - - + -
131B LYS* 2.9 32.7 + - - +
149B CYS* 3.5 23.3 - - - -
150B GLU 3.8 2.2 - - - -
151B ALA* 4.1 11.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 98 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A HIS* 3.1 33.0 + - + -
8A PHE* 4.4 7.9 - - + +
96B ASP* 4.3 0.4 + - - -
97B ILE* 1.3 71.4 - - - +
99B ILE* 1.3 60.8 + - - +
100B ILE* 3.5 9.9 + - + +
131B LYS* 2.8 42.2 + - + +
133B THR* 4.0 26.0 - - + -
149B CYS* 3.4 4.4 - - - -
150B GLU* 2.9 33.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 99 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40B VAL* 5.0 8.1 - - + -
41B ALA* 4.4 7.9 - - + -
97B ILE* 4.4 5.8 - - + -
98B THR* 1.3 71.8 - - - +
100B ILE* 1.3 60.1 + - - +
101B ALA* 4.3 18.4 - - + -
106B MSE 4.2 25.8 - - + -
110B ILE* 4.9 1.3 - - + -
113B MSE 3.7 35.2 - - + -
130B VAL* 4.1 9.0 - - + -
131B LYS 2.8 14.6 + - - +
132B ALA* 3.2 8.8 - - + +
133B THR* 2.8 33.1 + - - +
147B ILE* 5.5 3.1 - - + -
148B ALA 3.8 10.3 - - - +
149B CYS* 4.1 13.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 100 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A PHE* 3.6 37.5 - - + -
8B PHE* 5.2 5.2 - - + -
98B THR* 3.6 17.9 - - + +
99B ILE* 1.3 75.2 - - - +
101B ALA* 1.3 61.7 + - - +
133B THR* 3.4 10.3 - - + +
135B THR* 3.7 30.5 - - + -
141B THR* 3.6 9.5 - - - +
147B ILE* 3.8 0.2 - - - -
148B ALA* 2.9 47.4 + - + +
149B CYS 5.0 0.7 - - - -
150B GLU* 4.4 20.2 - - + +
171B ACY 4.3 10.8 - - + -
----------------------------------------------------------
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