Contacts of the strand formed by residues 102 - 108 (chain B) in PDB entry 2IHU
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 VAL 102 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61B GLY 4.7 2.9 - - - +
64B ALA* 3.9 11.9 - - + +
65B ASP* 3.6 26.0 - - + +
68B ALA* 4.5 0.7 - - + -
75B GLN 3.5 6.1 - - - +
77B CYS* 3.8 29.4 - - - -
91B GLY 6.1 0.9 - - - +
92B ILE* 6.1 1.6 - - + -
95B SER* 3.7 15.9 - - - +
100B SER* 3.1 26.8 + - - +
101B PRO* 1.3 74.8 - - - +
103B ILE* 1.3 70.3 + - - +
104B ALA* 4.1 4.7 - - + +
162B GLY 3.7 2.7 + - - +
163B PRO* 3.0 7.7 - - + +
164B SER 2.8 26.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 103 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B LEU* 4.2 24.5 - - + -
74B PRO* 4.6 11.2 - - + -
75B GLN 2.8 17.6 + - - +
76B ALA* 3.3 4.4 - - + +
77B CYS 3.1 24.8 + - - +
102B VAL* 1.3 78.4 - - - +
104B ALA* 1.3 60.2 + - - +
105B LEU* 3.9 24.0 + - + +
149B VAL* 5.4 3.1 - - + -
152B ALA* 3.9 32.8 - - + +
153B VAL* 3.8 31.2 - - + +
156B ALA* 4.1 7.6 - - + -
164B SER* 3.5 7.0 - - - +
166B ILE* 4.8 4.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 104 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77B CYS* 3.8 17.9 - - - -
88B LEU* 4.1 3.6 - - + -
92B ILE* 3.7 36.6 - - + -
102B VAL* 3.7 4.8 + - + +
103B ILE* 1.3 72.7 - - - +
105B LEU* 1.3 62.7 + - - +
163B PRO* 5.1 3.4 - - + -
164B SER 2.8 14.0 + - - +
165B PHE* 3.2 9.4 - - + -
166B ILE 3.0 24.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 105 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18B LEU* 4.2 15.0 - - + -
19B LEU* 6.4 0.2 - - + -
22B LEU* 3.9 27.8 - - + -
30B VAL* 5.2 2.0 - - + -
76B ALA* 4.6 5.2 - - + -
77B CYS 3.0 14.1 + - - +
78B TRP* 3.3 39.7 - - + -
79B ALA 3.0 23.6 + - - -
88B LEU* 4.0 3.5 - - - +
103B ILE* 3.9 23.8 - - + +
104B ALA* 1.3 77.6 - - - +
106B ALA* 1.3 62.8 + - - +
165B PHE* 4.5 0.9 - - - -
166B ILE* 3.6 32.5 - - + +
168B LEU* 4.1 7.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 106 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78B TRP* 5.4 0.7 - - - -
79B ALA* 3.2 12.6 - - + +
80B THR 4.0 1.6 - - - +
85B MET* 3.9 24.7 - - + -
88B LEU* 5.0 1.8 - - + -
105B LEU* 1.3 75.9 - - - +
107B ALA* 1.3 65.7 + - - +
165B PHE* 3.5 25.5 - - + -
166B ILE 3.1 7.4 + - - +
167B SER* 3.4 4.2 - - - -
168B LEU* 2.8 30.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 107 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B GLU* 3.6 46.7 - - + +
78B TRP* 5.0 4.0 - - + -
79B ALA 3.1 8.1 + - - -
80B THR 4.0 0.2 - - - -
81B LEU* 3.2 29.2 - - + +
106B ALA* 1.3 80.7 - - - +
108B GLN* 1.3 62.4 + - - +
125B SER* 4.9 4.0 + - - -
167B SER* 4.5 1.4 + - - -
168B LEU* 3.4 12.6 - - + +
170B VAL* 4.3 5.4 - - + -
173B LEU* 5.6 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 108 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81B LEU* 3.8 14.5 - - - +
107B ALA* 1.3 74.6 - - - +
109B SER* 1.3 96.3 + - - +
114B ILE* 3.9 20.9 - - + +
121B GLN 4.6 0.2 - - - +
122B CYS* 3.8 19.5 - - - -
123B LEU 2.9 26.2 + - - +
124B ASP* 4.9 1.0 - - - +
125B SER* 3.8 15.8 + - - +
138B GLU* 4.3 10.6 + - - +
167B SER* 3.3 22.0 + - - +
168B LEU 2.9 6.3 + - - -
169B PRO* 3.9 13.2 - - + -
170B VAL* 3.0 25.9 + - - +
----------------------------------------------------------
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