Contacts of the helix formed by residues 28 - 39 (chain A) 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 PRO 28 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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20A PRO 3.9 10.1 - - - +
21A LEU* 3.9 19.3 - - + +
22A LEU 3.9 5.8 - - - +
23A ASP* 4.6 0.9 - - + -
27A LYS* 1.3 83.8 - - - +
29A MET* 1.3 69.2 + - - +
30A ILE* 4.0 13.5 - - + -
31A GLN* 2.6 47.6 + - + +
32A HIS* 3.6 2.1 + - - -
58A ALA* 5.1 6.1 - - + +
62A PHE* 4.2 7.2 - - + -
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Residues in contact with MET 29 (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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19A LYS* 3.5 34.3 - - + +
20A PRO 3.3 8.5 + - - +
22A LEU* 3.0 19.8 + - - +
24A ILE* 4.1 7.9 - - + -
27A LYS 3.4 1.4 + - - -
28A PRO* 1.3 70.2 - - - +
30A ILE* 1.3 63.8 + - - +
32A HIS* 3.0 25.8 + - - +
33A VAL* 3.3 10.2 + - + +
97A GLY 3.4 13.0 - - - +
98A ASP* 3.3 37.2 - - + -
100A PRO* 4.0 18.4 - - + -
224A VAL* 3.7 37.2 - - + -
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Residues in contact with ILE 30 (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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7A ILE* 4.0 21.5 - - + -
9A ALA* 4.1 13.5 - - + -
20A PRO* 3.0 26.2 + - + +
21A LEU* 4.8 8.3 - - + -
28A PRO* 2.9 12.1 + - + -
29A MET* 1.3 76.8 - - - +
31A GLN* 1.3 59.1 + - - +
33A VAL* 3.5 5.1 + - + +
34A TYR* 3.0 26.0 + - - +
48A VAL* 3.7 35.4 - - + -
55A VAL* 5.2 2.0 - - + -
58A ALA* 5.0 2.9 - - + -
59A VAL* 4.1 14.8 - - + -
62A PHE* 3.8 16.2 - - + -
97A GLY* 4.5 11.0 - - - +
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Residues in contact with GLN 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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27A LYS* 3.3 30.8 - - + +
28A PRO* 2.6 42.9 + - + +
30A ILE* 1.3 73.2 - - - +
32A HIS* 1.3 60.3 + - - +
34A TYR* 3.1 0.7 + - - +
35A GLU* 2.8 64.0 + - + +
62A PHE* 3.5 46.3 - - + +
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Residues in contact with HIS 32 (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 ILE* 2.7 49.3 + - + +
25A VAL* 3.7 15.5 - - + -
27A LYS* 3.4 35.6 + - + +
28A PRO 3.6 4.2 + - - -
29A MET* 3.0 11.0 + - - +
31A GLN* 1.3 77.7 - - - +
33A VAL* 1.3 61.5 + - - +
35A GLU* 4.2 7.1 + - - +
36A ARG* 2.9 37.6 + - - +
100A PRO* 4.0 19.3 - - + +
237A MET* 4.1 20.8 - - + -
241A LEU* 6.4 1.1 - - + -
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Residues in contact with VAL 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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7A ILE* 3.8 25.8 - - + -
29A MET 3.3 12.4 + - - +
30A ILE* 3.8 7.4 - - - +
31A GLN 3.2 0.2 - - - -
32A HIS* 1.3 77.5 - - - +
34A TYR* 1.3 60.6 + - - +
36A ARG* 3.6 4.3 + - - +
37A ALA* 3.1 22.2 + - - +
95A LEU* 4.6 11.9 - - + +
96A GLN 3.6 18.8 - - - +
97A GLY* 3.8 20.4 - - - +
99A GLU 3.9 8.5 - - - +
100A PRO* 3.9 24.0 - - + -
102A ILE* 4.8 8.0 - - + +
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Residues in contact with TYR 34 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7A ILE* 4.1 7.6 - - + +
30A ILE 3.0 18.6 + - - +
31A GLN 3.1 3.8 + - - +
33A VAL* 1.3 75.2 - - - +
35A GLU* 1.3 67.1 + - + +
37A ALA* 3.0 13.3 + - - +
38A LEU* 3.1 43.7 + - + +
46A VAL* 2.9 41.7 + - + +
48A VAL* 3.4 32.3 - - + -
62A PHE* 3.6 23.1 - + + -
63A GLY 4.8 2.8 + - - -
64A GLY* 3.6 16.1 - - - -
65A LYS* 3.1 29.3 + - - +
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Residues in contact with GLU 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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27A LYS* 3.0 30.0 + - - +
31A GLN* 2.8 55.9 + - + +
32A HIS* 4.2 7.0 + - - +
34A TYR* 1.3 75.4 - - + +
36A ARG* 1.3 62.4 + - + +
38A LEU* 3.2 25.8 + - + +
39A GLN* 3.3 18.9 + - - +
62A PHE* 5.9 0.9 - - + -
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Residues in contact with ARG 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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32A HIS* 2.9 20.7 + - - +
33A VAL 4.0 3.4 - - - +
34A TYR 3.2 0.8 - - - -
35A GLU* 1.3 74.8 - - + +
37A ALA* 1.3 65.9 + - - +
39A GLN* 3.1 26.9 + - - +
40A VAL* 3.7 5.2 + - - +
100A PRO 3.3 20.2 + - - -
101A MET* 3.6 16.8 + - - +
102A ILE* 3.1 38.8 + - + -
103A ARG* 5.2 2.2 - - - +
104A PRO* 3.4 27.8 - - + +
237A MET* 3.4 25.5 - - - -
240A GLU* 3.3 27.5 + - - +
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Residues in contact with ALA 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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5A ILE* 3.8 16.5 - - + +
7A ILE* 4.3 1.8 - - + -
33A VAL 3.1 14.5 + - - +
34A TYR 3.0 10.4 + - - +
36A ARG* 1.3 77.1 - - - +
38A LEU* 1.3 61.3 + - - +
40A VAL* 3.2 29.0 + - - +
43A VAL* 5.2 1.4 - - - +
46A VAL* 3.9 24.7 - - + +
95A LEU* 3.8 22.2 - - + -
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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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34A TYR* 3.1 44.7 + - + +
35A GLU* 3.4 16.8 - - + +
36A ARG 3.1 0.6 - - - -
37A ALA* 1.3 77.8 - - - +
39A GLN* 1.3 58.9 + - + +
40A VAL 3.2 6.6 + - - +
46A VAL* 4.2 20.4 - - + -
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Residues in contact with GLN 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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35A GLU* 3.3 23.3 + - - +
36A ARG* 3.1 28.5 + - - +
38A LEU* 1.3 76.9 - - + +
40A VAL* 1.3 61.7 + - - +
41A ALA* 3.5 3.8 + - - +
104A PRO* 3.8 19.3 - - + +
105A ARG* 4.0 13.9 + - - +
108A GLU* 3.7 6.8 - - - +
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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