Contacts of the strand formed by residues 34 - 39 (chain A) in PDB entry 5GGR
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 MET 34 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A LEU* 3.6 28.0 - - + -
22A CYS* 4.6 2.2 - - - -
29A PHE* 3.4 38.4 - - + -
32A SER* 4.9 2.0 - - - +
33A GLY* 1.3 81.4 - - - +
35A HIS* 1.3 65.1 + - - +
50A VAL* 3.2 9.6 - - - +
51A ILE* 3.1 34.5 + - + -
70A ILE* 5.0 0.4 - - - -
72A ARG* 3.4 13.9 - - - +
79A LEU* 3.6 38.6 - - + -
96A CYS* 4.1 1.8 - - + -
97A ALA 3.5 17.3 - - - +
98A THR* 3.5 18.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 35 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A GLY 5.4 0.2 - - - -
34A MET* 1.3 74.9 - - - +
36A TRP* 1.3 69.3 + - - +
37A VAL* 4.8 5.8 - - + +
47A TRP* 2.7 35.8 + + - +
49A ALA 3.5 4.3 - - - -
50A VAL* 3.4 28.3 - - + +
70A ILE* 5.0 0.2 - - - -
79A LEU* 3.9 3.1 - - - +
96A CYS* 3.5 9.7 - - - +
97A ALA* 2.7 42.3 + - + +
98A THR 4.8 1.1 - - - -
99A ASN* 3.9 22.8 + - + -
103A TRP* 6.5 0.2 - - + -
89B GLN* 5.8 0.8 + - - -
94B TRP* 3.8 12.3 - + - -
96B ARG* 3.5 32.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 36 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A GLU* 4.6 6.1 - - + -
20A LEU* 4.1 18.4 - - + -
21A ASP 5.0 0.9 - - - -
22A CYS* 3.9 24.9 - - + -
35A HIS* 1.3 74.3 - - - +
37A VAL* 1.3 65.3 + - - +
47A TRP* 4.0 1.2 - - - -
48A VAL* 2.9 35.2 + - + -
49A ALA* 2.8 25.2 + - + +
70A ILE* 3.6 28.7 - - + -
79A LEU* 3.3 29.8 - - + +
80A PHE 3.7 3.2 + - - -
81A LEU* 3.4 44.7 - - + +
94A TYR* 3.6 30.7 - - + -
95A TYR 3.1 37.5 - - - -
96A CYS* 3.6 3.8 - - + -
107A THR* 5.2 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 37 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A HIS* 4.8 7.6 - - + +
36A TRP* 1.3 82.6 - - - +
38A ARG* 1.3 63.4 + - - +
45A LEU* 3.5 23.1 - - + -
46A GLU 3.4 7.2 - - - +
47A TRP* 4.3 11.7 - - + -
48A VAL* 3.7 2.7 - - - -
94A TYR* 4.4 2.0 - - - -
95A TYR* 2.8 41.4 + - - +
97A ALA* 5.6 1.3 - - + -
103A TRP* 3.5 28.9 - - + -
89B GLN* 5.9 0.7 - - - +
98B PHE* 3.4 35.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 38 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A VAL* 1.3 79.1 - - - +
39A GLN* 1.3 64.6 + - - +
40A ALA 5.4 0.4 - - - +
45A LEU* 3.7 0.2 - - - -
46A GLU* 3.0 71.7 + - + +
47A TRP 5.6 0.2 + - - -
48A VAL* 3.2 15.3 - - + +
61A ALA* 5.6 0.6 - - - +
63A SER* 3.5 22.0 - - - -
64A VAL* 4.2 13.1 - - - +
68A PHE* 4.5 2.6 - - - -
89A GLU 4.6 3.4 + - - -
90A ASP* 2.9 36.4 + - - +
92A ALA* 3.5 19.1 - - + -
93A VAL 3.0 7.6 - - - +
94A TYR* 3.4 40.3 + - + -
95A TYR* 5.1 0.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 39 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A ARG* 1.3 78.9 - - - +
40A ALA* 1.3 67.6 + - - +
41A PRO* 3.7 0.9 - - + +
42A GLY 5.9 0.7 - - - -
43A LYS 2.7 30.9 + - - +
44A GLY 3.4 14.8 - - - +
45A LEU* 4.0 10.0 - - + +
46A GLU* 4.8 1.3 - - - +
92A ALA* 3.1 6.1 - - - -
93A VAL* 2.9 35.1 + - + +
95A TYR* 3.7 21.9 + - + -
38B GLN* 3.4 20.1 + - - +
87B TYR* 3.3 21.8 + - - -
----------------------------------------------------------
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