Contacts of the strand formed by residues 30 - 39 (chain A) 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 LEU 30 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28A PRO* 3.6 0.4 - - - +
29A GLU* 1.3 92.2 - - + +
31A ALA* 1.3 61.2 + - - +
64A VAL* 3.2 6.2 - - - +
65A GLY 2.8 29.5 + - - +
67A PRO* 4.4 12.1 - - + -
152A PHE* 3.6 21.8 - - + -
155A GLN* 3.8 35.7 - - + +
156A LEU* 3.8 29.6 - - + -
389A VAL* 6.4 0.9 - - + -
390A LEU 5.2 0.2 - - - -
392A LEU* 3.7 4.1 - - - +
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Residues in contact with ALA 31 (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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13A LEU* 3.7 19.1 - - + -
30A LEU* 1.3 78.2 - - - +
32A VAL* 1.3 68.1 + - - +
63A LEU 3.3 6.3 - - - -
64A VAL* 4.2 2.7 - - + -
152A PHE* 5.5 0.7 - - - -
155A GLN* 5.2 1.0 - - - +
389A VAL* 3.7 6.5 - - - +
390A LEU* 2.9 51.1 + - + +
392A LEU* 3.6 18.8 - - + +
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Residues in contact with VAL 32 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A ALA* 1.3 79.6 - - - +
33A SER* 1.3 64.0 + - - +
62A VAL* 3.3 7.1 - - - +
63A LEU* 2.8 45.1 + - + +
148A ALA* 3.2 34.5 - - + +
151A THR* 3.2 44.2 - - + +
152A PHE* 3.9 9.0 - - + +
155A GLN* 4.6 4.0 - - + -
388A LYS 3.7 9.6 - - - +
389A VAL* 4.1 6.3 - - + -
390A LEU* 4.0 5.9 - - - +
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Residues in contact with SER 33 (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 VAL* 5.1 1.1 - - - +
32A VAL* 1.3 80.8 - - - +
34A ALA* 1.3 62.7 + - - +
35A PRO* 4.9 0.2 - - - -
60A MET* 3.9 22.7 - - - -
61A THR 3.3 10.8 - - - -
62A VAL* 4.2 2.7 - - - -
151A THR* 4.9 0.7 + - - -
386A GLY 5.2 1.0 + - - -
387A ALA* 3.2 4.0 - - - +
388A LYS* 3.0 53.8 + - - +
390A LEU* 3.8 17.9 - - - +
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Residues in contact with ALA 34 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A SER* 1.3 77.0 - - - +
35A PRO* 1.3 68.2 - - + +
60A MET* 4.2 3.4 - - - -
61A THR 2.9 20.4 + - - +
144A SER* 2.8 27.0 + - - +
147A VAL* 4.0 9.0 - - + -
148A ALA* 3.4 31.6 - - + +
190A SER* 3.8 12.8 - - - +
387A ALA* 4.1 1.3 - - + +
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Residues in contact with PRO 35 (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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34A ALA* 1.3 86.6 - - - +
36A GLY* 1.3 66.0 + - - +
56A ALA* 3.8 11.7 - - + -
57A LEU 3.4 21.8 - - - +
59A LEU 3.5 6.7 - - - +
60A MET* 4.3 5.4 - - + -
140A SER 4.8 0.2 - - - +
144A SER* 3.6 10.0 + - - -
190A SER* 2.9 45.8 + - - +
385A ASP 3.1 22.2 - - - +
386A GLY* 3.6 16.4 - - - +
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Residues in contact with GLY 36 (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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35A PRO* 1.3 78.1 - - - +
37A ARG* 1.3 63.0 + - - +
56A ALA* 3.6 5.7 - - - -
57A LEU* 3.0 27.2 + - - -
59A LEU* 2.9 17.2 + - - -
133A VAL* 4.0 15.2 - - - +
139A LEU 3.4 11.2 - - - -
140A SER* 4.1 6.5 - - - -
144A SER* 4.4 0.2 - - - -
190A SER* 5.5 1.0 - - - -
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Residues in contact with ARG 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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36A GLY* 1.3 75.9 - - - +
38A VAL* 1.3 77.0 + - - +
39A ASN* 3.9 6.3 - - - +
43A GLU* 5.7 0.8 + - - -
54A PRO* 3.9 8.1 - - + -
55A MET 3.7 7.6 - - - +
57A LEU* 3.7 7.2 - - - +
138A GLY 2.1 35.8 + - - -
139A LEU* 2.8 31.2 + - - +
140A SER* 3.3 14.6 - - - +
185A MET* 4.3 14.9 - - - -
186A ASP* 2.3 50.9 + - - +
189A ILE* 3.4 31.9 - - + -
190A SER* 6.0 0.9 - - - -
344A THR* 4.7 0.6 - - - -
345A GLY* 3.6 25.0 - - - +
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Residues in contact with VAL 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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37A ARG* 1.3 82.0 - - - +
39A ASN* 1.3 62.7 + - - +
40A LEU* 3.6 8.8 + - + -
54A PRO* 3.4 0.5 - - - +
55A MET* 3.0 46.2 + - + +
57A LEU* 3.6 21.3 - - + +
139A LEU* 4.5 5.6 - - + -
220A VAL* 4.9 0.2 - - + -
222A ILE* 3.9 23.1 - - + -
344A THR* 3.8 14.8 - - + +
353A VAL* 3.8 31.6 - - + -
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Residues in contact with ASN 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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37A ARG* 3.9 7.4 - - - +
38A VAL* 1.3 73.8 - - - +
40A LEU* 1.3 67.1 + - - +
41A ILE 2.8 20.9 + - - +
42A GLY 3.1 27.5 + - - -
43A GLU* 2.8 33.7 + - - +
52A VAL* 4.6 0.2 - - - +
53A LEU 3.3 7.6 + - - -
54A PRO* 4.0 3.4 - - - -
185A MET* 2.9 33.3 - - + +
342A ARG* 3.2 2.1 + - - -
344A THR* 2.7 35.1 - - + +
345A GLY 5.0 1.3 - - - +
353A VAL* 3.9 0.2 - - - +
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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