Contacts of the strand formed by residues 54 - 68 (chain D) in PDB entry 6GR2
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 PRO 54 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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37D ARG* 4.4 3.4 - - - -
38D VAL 3.3 13.5 - - - +
39D ASN* 4.0 1.8 - - - -
40D LEU* 4.8 0.7 - - - -
52D VAL* 3.4 8.5 - - + -
53D LEU* 1.3 92.4 - - - +
55D MET* 1.3 59.3 + - - +
185D MET* 3.0 30.5 - - + -
189D ILE* 3.9 20.4 - - + -
198D ALA* 3.6 2.2 - - - -
199D LEU* 2.8 45.8 + - - +
201D ILE* 3.8 19.7 - - + -
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Residues in contact with MET 55 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37D ARG* 3.5 2.1 - - - +
38D VAL* 3.0 43.7 + - + +
40D LEU* 4.5 19.2 - - + +
54D PRO* 1.3 74.9 - - - +
56D ALA* 1.3 69.2 + - - +
57D LEU* 4.0 21.3 - - + -
189D ILE* 3.9 8.1 - - - -
197D HIS 3.9 19.7 - - - +
198D ALA* 4.2 7.6 - - + -
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Residues in contact with ALA 56 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35D PRO* 3.7 26.5 - - + -
36D GLY 3.5 5.8 - - - +
55D MET* 1.3 84.9 - - - +
57D LEU* 1.3 62.2 - - - +
189D ILE* 3.7 22.1 - - + +
193D GLY* 4.3 15.2 - - - -
194D GLN 6.1 1.1 - - - +
197D HIS 5.0 2.2 + - - -
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Residues in contact with LEU 57 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35D PRO* 3.3 21.7 - - - +
36D GLY 2.8 15.5 + - - +
37D ARG 3.8 31.6 - - - +
38D VAL* 3.7 23.8 - - + +
55D MET* 4.0 16.8 - - + -
56D ALA* 1.3 74.9 - - - +
58D GLU* 1.3 64.0 + - - +
59D LEU* 3.2 19.9 - - + +
60D MET* 5.6 0.2 - - - +
139D LEU* 3.9 32.5 - - + -
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Residues in contact with GLU 58 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6D GLN* 4.8 17.9 - - + +
7D PRO 4.3 10.5 - - - +
8D GLN* 5.8 1.7 + - - -
57D LEU* 1.3 73.1 - - - +
59D LEU* 1.3 64.9 + - - +
60D MET* 3.6 18.8 + - - +
132D SER* 4.4 0.5 + - - -
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Residues in contact with LEU 59 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5D ARG 5.3 2.2 - - - +
6D GLN* 4.4 22.7 - - + -
7D PRO* 5.1 1.1 - - + +
35D PRO* 3.5 0.9 - - - +
36D GLY* 2.9 24.0 + - - +
57D LEU* 3.2 20.0 - - + +
58D GLU* 1.3 79.2 - - - +
60D MET* 1.3 58.5 + - - +
132D SER* 3.5 27.1 - - - +
133D VAL* 3.5 12.3 - - + -
134D PRO* 3.7 26.7 - - + -
139D LEU* 3.7 19.7 - - + -
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Residues in contact with MET 60 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7D PRO 4.7 1.3 - - - +
8D GLN* 4.6 1.3 - - - -
9D VAL* 4.0 33.2 - - + +
12D LEU* 3.6 26.0 - - + +
33D SER* 3.5 26.0 - - - -
34D ALA 3.5 16.8 - - - +
35D PRO* 4.3 4.5 - - + -
58D GLU 3.8 12.8 - - - +
59D LEU* 1.3 75.2 - - - +
61D THR* 1.3 73.1 + - - +
62D VAL* 4.1 2.5 - - - -
131D SER* 3.2 3.6 + - - -
132D SER* 2.9 31.5 + - - -
133D VAL* 3.3 6.3 - - - +
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Residues in contact with THR 61 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33D SER* 3.1 6.1 - - - -
34D ALA 2.8 33.8 + - - -
60D MET* 1.3 71.2 - - - +
62D VAL* 1.3 65.9 + - - +
63D LEU* 4.2 0.4 + - + -
129D VAL* 3.6 29.6 - - + -
130D VAL 3.5 4.0 - - - +
131D SER* 3.2 16.8 + - - -
133D VAL* 4.3 0.2 - - - +
141D SER* 4.5 1.9 + - - -
144D SER* 2.7 35.8 + - - +
145D LEU* 4.0 9.8 + - + +
148D ALA* 3.8 19.3 - - + +
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Residues in contact with VAL 62 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9D VAL* 4.7 7.0 - - + -
12D LEU* 3.7 31.2 - - + -
13D LEU* 4.2 34.5 - - + +
16D ALA* 4.2 5.0 - - + +
32D VAL 3.3 9.6 - - - +
33D SER* 4.2 13.5 - - - -
60D MET* 4.3 6.1 - - - -
61D THR* 1.3 78.4 - - - +
63D LEU* 1.3 62.9 + - - +
64D VAL* 4.2 9.2 - - + -
128D VAL 3.8 1.2 - - - +
129D VAL* 3.6 3.3 - - - +
130D VAL* 2.8 45.2 + - + +
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Residues in contact with LEU 63 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30D LEU 4.0 0.2 - - - +
31D ALA* 3.4 2.1 - - - -
32D VAL* 2.8 47.0 + - + +
61D THR 4.2 0.6 + - - -
62D VAL* 1.3 73.9 - - - +
64D VAL* 1.3 65.8 + - - +
75D LEU* 6.4 0.9 - - + -
125D PHE* 6.1 2.0 - - + -
127D ALA* 3.5 24.5 - - + -
128D VAL 3.5 8.3 - - - +
129D VAL* 4.1 21.5 - - + -
145D LEU* 5.5 0.9 - - + -
148D ALA* 4.6 6.7 - - + -
149D THR* 4.0 37.0 - - + +
152D PHE* 3.2 35.8 - - + -
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Residues in contact with VAL 64 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13D LEU* 3.7 31.0 - - + -
16D ALA* 3.6 23.6 - - + +
17D ARG* 4.7 4.7 - - + -
20D PHE* 4.0 3.9 - - + -
28D PRO* 3.8 21.1 - - + -
30D LEU 3.1 8.5 - - - +
31D ALA* 4.0 7.2 - - + -
62D VAL* 4.2 2.0 - - + -
63D LEU* 1.3 82.6 - - - +
65D GLY* 1.3 59.4 + - - +
127D ALA* 3.0 2.9 - - - +
128D VAL* 2.8 54.3 + - + -
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Residues in contact with GLY 65 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20D PHE* 3.6 9.4 - - - -
28D PRO* 4.0 1.4 - - - +
29D GLU 3.2 2.3 + - - -
30D LEU* 2.9 33.5 + - - +
64D VAL* 1.3 77.2 - - - +
66D SER* 1.3 65.6 + - - -
126D SER 2.8 15.3 - - - -
127D ALA* 3.8 1.1 - - - -
152D PHE* 3.6 15.1 - - - -
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Residues in contact with SER 66 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20D PHE* 3.8 11.4 - - - -
27D GLU 3.9 1.9 + - - -
28D PRO* 3.6 6.4 - - - +
29D GLU* 3.1 37.6 + - - +
30D LEU* 4.9 0.4 - - - -
65D GLY* 1.3 71.2 + - - -
67D PRO* 1.3 78.1 - - - +
68D ARG* 4.3 0.5 - - - +
125D PHE* 3.1 6.7 - - - +
126D SER* 2.8 31.8 + - - -
152D PHE* 4.0 1.2 - - - -
156D LEU* 4.8 1.8 - - - -
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Residues in contact with PRO 67 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29D GLU* 4.0 16.6 - - - +
30D LEU* 4.2 18.2 - - + -
66D SER* 1.3 94.6 - - - +
68D ARG* 1.3 64.3 + - - +
123D PRO* 4.5 10.3 - - + -
124D GLY 3.4 9.0 - - - +
125D PHE* 4.1 2.9 - - + -
156D LEU* 4.1 13.4 - - + -
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Residues in contact with ARG 68 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88C LEU* 5.5 4.2 - - - +
89C GLN* 2.9 36.6 + - - +
24D PHE* 4.5 6.1 - - - -
66D SER 4.3 0.2 - - - +
67D PRO* 1.3 79.6 - - - +
69D LYS* 1.3 61.3 + - - +
70D ASP* 3.0 35.2 + - + +
71D GLY 4.6 0.3 + - - -
72D LEU* 3.6 17.1 + - - +
74D SER* 4.1 14.5 - - - +
123D PRO* 4.1 8.1 - - - +
124D GLY* 2.7 29.7 + - - +
125D PHE* 3.3 22.2 - - - -
126D SER* 2.8 32.2 + - - +
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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