Contacts of the strand formed by residues 36 - 46 (chain A) in PDB entry 2GRR
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 36 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10A ALA* 6.1 1.3 - - + -
13A ARG* 3.2 48.5 - - - +
28A PRO* 4.1 18.4 - - + +
29A THR 3.7 5.4 - - - +
30A LYS* 3.6 25.4 - - + +
31A ASN* 3.1 11.9 + - - -
35A THR* 1.3 75.7 + - - +
37A ASN* 1.3 60.1 + - - +
38A LEU* 3.6 25.9 + - + +
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Residues in contact with ASN 37 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28A PRO* 3.7 3.1 - - - +
29A THR* 2.8 33.2 + - - +
30A LYS 4.3 1.9 - - - +
31A ASN* 3.3 26.7 + - - +
35A THR 3.7 0.6 + - - -
36A MET* 1.3 70.0 - - - +
38A LEU* 1.3 62.1 + - - +
39A MET* 3.0 32.5 + - - +
40A ASN* 3.1 35.3 + - - +
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Residues in contact with LEU 38 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6A LEU* 3.8 46.4 - - + +
9A LEU* 3.3 35.0 - - + +
10A ALA* 3.9 15.5 - - + +
13A ARG* 4.3 4.5 - - - -
28A PRO* 3.8 24.7 - - + -
36A MET* 3.6 32.0 + - + +
37A ASN* 1.3 72.9 - - - +
39A MET* 1.3 59.1 + - - +
40A ASN 3.3 0.7 - - - -
41A TRP* 2.7 25.1 + - - +
64A PHE* 3.8 1.0 - - - -
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Residues in contact with MET 39 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2A SER* 4.2 6.3 - - - +
5A ALA* 4.0 11.4 - - + -
6A LEU* 3.7 22.9 - - + -
9A LEU* 3.7 19.3 - - - -
37A ASN* 3.0 14.9 - - - +
38A LEU* 1.3 79.3 - - - +
40A ASN* 1.3 59.3 + - - +
63A LEU* 3.5 4.9 - - - +
64A PHE* 2.9 49.1 + - + +
65A LYS 3.3 31.0 - - - +
66A ASP* 3.7 19.3 - - - +
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Residues in contact with ASN 40 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29A THR* 2.8 44.1 + - - +
37A ASN* 3.1 18.6 + - - +
38A LEU 3.3 0.6 - - - -
39A MET* 1.3 80.9 - - + +
41A TRP* 1.3 63.3 + - - +
61A ARG* 2.9 39.1 + - - +
62A MET 3.5 3.4 - - - -
63A LEU* 3.4 22.6 - - + +
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Residues in contact with TRP 41 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9A LEU* 3.9 22.2 - - + +
12A GLU 4.1 0.7 - - - -
13A ARG* 3.6 28.9 - - + -
16A TRP* 4.9 5.2 - - + -
26A ALA* 3.7 41.5 - - + -
27A VAL 3.5 4.7 - - - +
28A PRO* 3.6 24.8 - - + +
38A LEU* 2.7 34.3 + - + +
40A ASN* 1.3 78.9 + - - +
42A GLU* 1.3 63.8 + - - +
43A CYS* 3.8 12.0 + - - -
61A ARG* 3.3 7.4 - - - +
62A MET* 2.9 42.7 + - + +
64A PHE* 3.6 20.3 - + - -
109A ILE* 3.5 31.0 - - + -
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Residues in contact with GLU 42 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25A VAL* 4.3 2.8 - - - +
26A ALA* 3.7 0.9 + - - -
27A VAL* 2.9 43.1 + - + +
29A THR* 3.4 24.0 - - + +
41A TRP* 1.3 71.0 - - - +
43A CYS* 1.3 60.9 + - - +
60A LEU 3.9 4.0 - - - -
61A ARG* 3.6 30.0 + - + +
78A GLU* 5.6 0.9 - - - +
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Residues in contact with CYS 43 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25A VAL* 3.0 12.8 - - - +
26A ALA* 3.8 18.4 - - - -
41A TRP* 4.1 11.9 - - - -
42A GLU* 1.3 79.9 - - - +
44A ALA* 1.3 63.5 + - - +
59A LYS* 3.4 8.1 - - - +
60A LEU* 2.8 47.6 + - + +
62A MET* 3.6 37.5 - - - -
113A LEU* 4.3 7.2 - - + -
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Residues in contact with ALA 44 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24A PHE* 3.4 9.2 - - - +
25A VAL* 2.9 46.8 + - + +
43A CYS* 1.3 77.2 - - - +
45A ILE* 1.3 65.9 + - - +
46A PRO 4.2 0.2 - - - -
57A LEU* 3.8 28.9 - - + -
58A PHE 3.4 7.6 - - - +
59A LYS* 4.6 9.2 - - + -
60A LEU* 4.6 0.2 - - - -
113A LEU* 5.2 0.3 - - - +
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Residues in contact with ILE 45 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24A PHE* 3.8 11.2 - - + -
44A ALA* 1.3 76.4 - - - +
46A PRO* 1.3 76.9 - - - +
57A LEU* 3.9 2.0 - - - -
58A PHE* 2.9 46.0 + - + +
60A LEU* 3.5 27.8 - - + -
77A PHE* 4.6 3.1 - - + -
113A LEU* 3.7 21.8 - - + +
116A ILE* 3.5 35.9 - - + -
117A GLN* 3.6 26.2 - - + -
120A LEU* 4.3 8.5 - - + -
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Residues in contact with PRO 46 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22A PHE 4.3 4.9 - - - +
23A GLY* 3.6 26.7 - - - +
24A PHE* 3.6 39.0 - - + -
45A ILE* 1.3 87.8 - - - +
47A GLY* 1.3 66.7 + - - +
48A LYS 3.5 0.2 + - - -
56A GLY 3.5 7.4 - - - +
57A LEU* 4.0 6.9 - - + -
58A PHE* 4.6 0.2 - - - -
117A GLN* 2.9 32.5 + - - +
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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
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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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