Contacts of the strand formed by residues 35 - 40 (chain B) in PDB entry 2G73
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 PHE 35 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34B ALA* 1.3 75.0 - - - +
36B SER* 1.3 69.4 + - - +
37B SER 4.4 0.2 - - - -
66B VAL* 4.1 15.3 - - + -
67B CYS* 3.3 9.0 - - - +
68B GLY* 2.8 63.0 + - - +
69B HIS 3.7 2.9 - - - -
70B PRO* 4.0 5.2 - - + -
76B ASN* 4.7 5.6 - - + +
79B ALA* 3.4 44.9 - - + -
80B VAL* 3.3 32.5 - - + -
83B ARG* 3.5 17.9 - - + -
118B CYS* 3.5 8.7 - - - -
119B PRO* 3.5 13.0 - - + +
121B PHE* 4.1 14.6 - - + -
186B EIP 3.9 1.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 36 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35B PHE* 1.3 78.0 - - - +
37B SER* 1.3 59.7 + - - +
38B TRP* 4.0 0.9 + - - -
64B ASN* 3.1 17.7 + - - -
66B VAL 3.6 5.2 - - - -
67B CYS* 3.8 11.7 - - - -
118B CYS* 3.7 8.3 - - - -
119B PRO 3.2 5.9 + - - +
120B VAL* 3.3 6.8 - - - +
121B PHE* 2.9 25.3 + - - -
161B TRP* 4.8 0.4 - - - -
165B GLN* 2.9 41.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 37 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35B PHE* 4.6 2.9 - - - -
36B SER* 1.3 77.0 + - - +
38B TRP* 1.3 66.4 + - - +
39B LEU* 3.7 14.7 - - - +
64B ASN* 3.1 13.7 - - - +
65B SER* 3.4 3.5 - - - -
66B VAL* 2.6 46.4 + - - -
80B VAL* 3.8 23.8 - - - +
121B PHE* 3.4 18.0 + - - +
122B ALA* 4.3 2.4 + - - -
123B ALA* 4.9 0.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 38 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B SER* 1.3 79.8 + - - +
39B LEU* 1.3 61.9 + - - +
40B PHE* 3.6 10.0 - + + -
46B LEU* 3.7 35.2 - - + -
64B ASN* 3.6 22.2 - - + -
65B SER* 3.6 4.0 - - - +
98B ILE* 4.9 0.6 - - - +
120B VAL* 3.6 20.5 - - + +
121B PHE 3.0 10.2 + - - +
122B ALA* 3.2 3.9 - - + -
123B ALA 3.1 23.4 + - - +
144B LEU* 4.8 4.5 - - + -
147B VAL* 5.0 2.7 - - + -
148B LEU* 5.7 0.4 - - + -
151B ILE* 4.9 0.9 - - + -
162B MET* 3.8 42.8 - - + -
165B GLN* 2.9 32.7 + - + +
166B ALA* 4.0 15.7 - - + -
175B LEU* 3.5 43.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 39 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B SER* 3.7 20.0 - - - +
38B TRP* 1.3 73.3 - - - +
40B PHE* 1.3 60.3 + - - +
46B LEU* 3.3 5.4 - - - +
47B LEU* 2.8 39.0 + - + -
65B SER* 2.7 23.7 + - - +
66B VAL* 3.9 9.6 - - + -
84B CYS* 3.6 26.5 - - - -
88B LEU* 4.0 17.9 - - + -
90B VAL* 4.1 12.8 - - + -
92B ILE* 4.1 11.2 - - + -
123B ALA* 3.4 22.9 - - + +
125B THR* 4.2 15.3 - - + -
141B TRP* 4.7 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 40 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B TRP* 3.6 28.0 - - + -
39B LEU* 1.3 75.6 - - - +
41B ASN* 1.3 67.3 - - - +
44B GLY 3.6 17.9 - - - -
45B GLN 3.0 9.0 - - - +
46B LEU* 3.9 24.2 - - + -
122B ALA* 4.4 2.0 - - + -
123B ALA 3.1 8.3 + - - -
124B ARG* 3.2 14.9 - - - -
125B THR* 3.0 24.1 + - - -
141B TRP* 4.1 0.9 - - - -
144B LEU* 4.7 6.5 - - + -
175B LEU* 3.6 45.3 - - + -
178B PHE* 3.4 38.6 - + + +
179B THR* 4.4 8.3 - - + -
----------------------------------------------------------
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