Contacts of the helix formed by residues 71 - 82 (chain A) in PDB entry 1GQ5
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 THR 71 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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35A LEU* 5.6 6.7 - - + -
37A GLN* 4.4 0.4 - - - -
70A GLU* 1.3 75.5 - - - +
72A HIS* 1.3 66.5 + - - +
73A GLN* 3.4 9.8 + - - +
74A GLN* 3.0 38.6 + - - +
75A VAL* 3.0 22.2 + - - +
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Residues in contact with HIS 72 (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 LEU* 3.1 28.5 - - + -
29A HIS* 4.2 4.4 - - - -
30A GLY 4.5 2.2 + - - +
37A GLN* 2.7 41.9 + - - +
71A THR* 1.3 73.9 - - - +
73A GLN* 1.3 60.9 + - + +
75A VAL* 3.4 1.4 + - - +
76A VAL* 3.1 53.0 + - + +
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Residues in contact with GLN 73 (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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71A THR* 3.1 8.9 + - - +
72A HIS* 1.3 81.1 - - + +
74A GLN* 1.3 65.0 + - + +
76A VAL* 4.1 4.5 - - - +
77A SER* 3.0 33.9 + - - +
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Residues in contact with GLN 74 (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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70A GLU* 3.1 36.7 + - + +
71A THR* 3.0 44.5 + - - +
73A GLN* 1.3 76.1 - - + +
75A VAL* 1.3 65.4 + - - +
77A SER* 3.3 6.1 + - - -
78A ARG* 3.0 28.6 + - - +
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Residues in contact with VAL 75 (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 LEU* 3.8 14.4 - - + -
37A GLN* 4.2 10.3 - - + -
59A LEU* 3.7 31.0 - - + -
62A VAL* 4.0 10.5 - - + -
67A VAL* 3.5 35.0 - - + +
70A GLU* 3.9 11.2 - - + +
71A THR 3.0 16.5 + - - +
72A HIS 4.1 2.2 - - - +
74A GLN* 1.3 78.3 - - - +
76A VAL* 1.3 62.7 + - - +
78A ARG* 3.2 8.0 + - - +
79A ILE* 3.0 24.4 + - + +
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Residues in contact with VAL 76 (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 LEU* 4.1 14.6 - - + -
72A HIS* 3.1 50.7 + - + +
73A GLN* 4.1 4.0 - - - +
75A VAL* 1.3 74.1 - - - +
77A SER* 1.3 59.5 + - - +
79A ILE* 3.2 8.2 + - + +
80A ARG* 2.8 70.5 + - + +
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Residues in contact with SER 77 (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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73A GLN* 3.0 28.2 + - - +
74A GLN* 3.5 6.9 - - - -
76A VAL* 1.3 79.0 - - - +
78A ARG* 1.3 58.2 + - - +
80A ARG* 3.4 5.3 + - - +
81A ALA* 2.9 32.8 + - - +
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Residues in contact with ARG 78 (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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62A VAL* 4.4 17.8 + - + +
63A ASN* 5.0 1.7 + - - -
65A GLU* 3.6 35.6 + - - +
66A ASN 5.6 1.0 + - - -
67A VAL* 3.6 23.5 - - - +
70A GLU* 2.9 30.4 + - - -
74A GLN* 3.0 18.5 + - - +
75A VAL* 3.2 6.7 + - - +
77A SER* 1.3 74.1 - - - +
79A ILE* 1.3 69.4 + - - +
81A ALA* 3.1 12.9 + - - +
82A ALA* 3.4 10.7 + - - +
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Residues in contact with ILE 79 (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* 5.0 0.3 + - - -
24A TYR* 4.1 28.7 - - + -
26A PHE* 4.6 18.2 - - + -
28A LEU* 3.9 26.0 - - + -
59A LEU* 4.0 11.0 - - + -
62A VAL* 3.9 24.9 - - + -
75A VAL* 3.0 20.3 + - + +
76A VAL* 3.7 8.5 - - + +
78A ARG* 1.3 76.8 - - - +
80A ARG* 1.3 67.6 + - + +
81A ALA 3.3 0.3 + - - -
82A ALA* 3.5 8.3 + - - +
86A VAL* 3.6 22.1 - - + +
88A LEU* 4.5 7.6 - - + -
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Residues in contact with ARG 80 (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* 4.1 19.7 + - - +
76A VAL* 2.8 44.7 + - + +
77A SER* 3.9 4.7 - - - +
79A ILE* 1.3 82.1 - - + +
81A ALA* 1.3 60.5 + - - +
82A ALA 3.4 6.8 - - - +
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Residues in contact with ALA 81 (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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77A SER 2.9 17.8 + - - +
78A ARG* 3.1 4.8 + - - +
80A ARG* 1.3 72.3 - - - +
82A ALA* 1.3 69.3 + - - +
83A LEU* 3.5 14.6 + - - +
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Residues in contact with ALA 82 (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* 4.8 5.5 + - - -
24A TYR* 4.8 3.3 + - - +
63A ASN* 3.6 20.6 - - - +
78A ARG 3.4 5.9 + - - +
79A ILE 3.9 2.7 - - - +
80A ARG 3.3 9.5 - - - +
81A ALA* 1.3 81.6 - - - +
83A LEU* 1.3 65.6 + - - +
85A ALA 3.3 24.9 - - - +
86A VAL* 3.6 11.9 - - + -
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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