Contacts of the helix formed by residues 29 - 39 (chain B) in PDB entry 1GQC
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 29 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19B LYS* 3.3 51.8 - - + +
20B PRO* 3.4 7.4 + - + +
22B LEU* 2.8 18.7 + - + +
24B ILE* 3.9 15.5 - - + -
27B LYS 3.4 1.0 + - - -
28B PRO* 1.3 69.5 - - - +
30B ILE* 1.3 64.5 + - - +
32B HIS* 2.9 25.0 + - - +
33B VAL* 3.2 9.7 + - - +
97B GLY 3.7 12.8 - - - +
98B ASP* 3.7 19.3 - - + -
100B PRO* 4.1 11.9 - - + -
224B VAL* 3.5 35.9 - - + -
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Residues in contact with ILE 30 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7B ILE* 3.9 19.5 - - + -
9B ALA* 3.7 17.9 - - + -
20B PRO* 3.0 31.6 + - + +
21B LEU* 4.8 7.9 - - + -
28B PRO* 4.2 11.2 - - + +
29B MET* 1.3 75.9 - - - +
31B GLN* 1.3 60.8 + - - +
33B VAL* 3.5 3.7 + - + +
34B TYR* 3.0 25.3 + - - +
48B VAL* 3.7 37.2 - - + -
55B VAL* 5.3 1.3 - - + -
58B ALA* 5.4 2.2 - - + -
59B VAL* 4.3 12.8 - - + -
62B PHE* 4.4 11.4 - - + -
97B GLY* 4.7 8.5 - - - +
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Residues in contact with GLN 31 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27B LYS* 3.6 27.9 - - + +
28B PRO* 2.7 41.4 + - + +
30B ILE* 1.3 73.0 - - - +
32B HIS* 1.3 57.5 + - - +
34B TYR* 3.7 0.2 - - - -
35B GLU* 2.8 66.6 + - + +
62B PHE* 3.5 53.0 - - + +
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Residues in contact with HIS 32 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24B ILE* 2.9 42.9 + - + +
25B VAL* 4.0 15.5 - - + -
27B LYS* 3.5 42.8 + - + +
28B PRO 3.5 4.7 + - - -
29B MET* 2.9 10.1 + - - +
31B GLN* 1.3 78.6 - - - +
33B VAL* 1.3 60.6 + - - +
35B GLU* 4.2 7.2 + - - +
36B ARG* 3.1 35.7 + - - +
100B PRO* 3.7 19.5 - - + +
237B MET* 3.9 18.7 - - + +
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Residues in contact with VAL 33 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7B ILE* 3.7 28.9 - - + -
29B MET 3.2 7.9 + - - +
30B ILE* 3.8 7.6 - - - +
31B GLN 3.2 0.4 - - - -
32B HIS* 1.3 77.4 - - - +
34B TYR* 1.3 57.7 + - - +
36B ARG* 3.5 4.1 + - - +
37B ALA* 3.0 26.5 + - - +
95B LEU* 4.7 10.8 - - + +
96B GLN 3.7 15.7 - - - +
97B GLY* 3.7 22.2 - - - +
99B GLU 3.7 23.8 - - - +
100B PRO* 3.8 13.0 - - + -
102B ILE* 4.9 6.1 - - + +
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Residues in contact with TYR 34 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7B ILE* 4.0 8.1 - - + -
30B ILE 3.0 17.7 + - - +
31B GLN 3.2 3.6 + - - +
33B VAL* 1.3 75.3 - - - +
35B GLU* 1.3 67.4 + - + +
37B ALA* 3.0 5.2 + - - +
38B LEU* 3.0 47.6 + - + +
46B VAL* 3.1 47.2 + - + +
48B VAL* 3.4 30.7 - - + -
62B PHE* 3.7 24.7 - + + -
63B GLY 4.9 1.7 + - - -
64B GLY* 3.6 13.4 - - - -
65B LYS* 3.0 33.5 + - - +
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Residues in contact with GLU 35 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27B LYS* 2.8 34.2 + - - +
31B GLN* 2.8 52.4 + - + +
32B HIS* 4.3 6.2 + - - +
34B TYR* 1.3 75.7 - - + +
36B ARG* 1.3 61.9 + - + +
38B LEU* 3.2 27.1 + - + +
39B GLN* 3.4 18.0 + - - +
62B PHE* 5.5 2.9 - - + -
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Residues in contact with ARG 36 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32B HIS* 3.1 21.2 + - - +
33B VAL 4.0 3.1 - - - +
34B TYR 3.2 0.4 - - - -
35B GLU* 1.3 76.0 - - + +
37B ALA* 1.3 66.1 + - - +
39B GLN* 3.0 34.2 + - - +
40B VAL* 3.7 4.7 + - - +
100B PRO 3.0 24.8 + - - -
101B MET* 3.7 9.9 + - - +
102B ILE* 2.9 37.9 + - + -
103B ARG* 4.9 2.6 - - - +
104B PRO* 3.6 23.3 - - + +
237B MET* 3.0 27.5 - - - +
240B GLU* 3.6 23.0 + - - -
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Residues in contact with ALA 37 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5B ILE* 3.7 14.9 - - + +
7B ILE* 4.3 2.2 - - + -
33B VAL 3.0 15.6 + - - +
34B TYR 3.0 9.8 + - - +
36B ARG* 1.3 76.4 - - - +
38B LEU* 1.3 61.6 + - - +
40B VAL* 3.2 25.5 + - - +
43B VAL* 5.3 0.7 - - - +
46B VAL* 3.7 28.4 - - + +
95B LEU* 3.7 23.5 - - + +
102B ILE* 5.8 0.4 - - - +
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Residues in contact with LEU 38 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34B TYR* 3.0 45.3 + - + +
35B GLU* 3.3 17.7 - - + +
36B ARG 3.0 0.4 - - - -
37B ALA* 1.3 78.7 - - - +
39B GLN* 1.3 57.8 + - + +
40B VAL 3.2 6.3 + - - +
46B VAL* 4.0 21.1 - - + +
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Residues in contact with GLN 39 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35B GLU* 3.5 21.2 + - - +
36B ARG* 3.0 28.5 + - - +
38B LEU* 1.3 76.0 - - + +
40B VAL* 1.3 62.1 + - - +
41B ALA* 3.4 3.6 + - - +
104B PRO* 3.9 21.8 - - + +
108B GLU* 3.7 7.1 - - - +
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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