Contacts of the helix formed by residues 75 - 86 (chain A) in PDB entry 1GZD
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 GLY 75 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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72A LYS 3.1 12.6 + - - -
73A SER 3.3 2.0 + - - -
74A ARG* 1.3 78.3 - - - +
76A VAL* 1.3 61.1 + - - +
77A GLU* 3.3 3.1 - - - -
78A ALA* 3.4 10.2 + - - +
79A ALA* 2.9 31.4 + - - +
82A ARG* 4.4 5.3 + - - -
502A VAL* 4.2 1.3 - - - +
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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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71A ALA* 3.1 39.7 + - + +
72A LYS 4.4 0.2 + - - -
74A ARG 5.0 0.2 - - - -
75A GLY* 1.3 73.7 - - - +
77A GLU* 1.3 69.8 + - - +
79A ALA* 3.8 1.8 - - - +
80A ARG* 3.0 30.0 + - + +
306A PHE* 5.5 2.0 - - + -
311A LEU* 4.6 11.9 - - + -
317A VAL* 4.6 13.0 - - + -
498A PHE* 5.1 2.8 - - + -
499A VAL* 4.2 27.8 - - + -
502A VAL* 4.1 17.0 - - + -
503A ILE* 3.9 21.3 - - + -
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Residues in contact with GLU 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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72A LYS* 3.5 46.4 - - - +
75A GLY* 3.3 1.0 - - - -
76A VAL* 1.3 81.3 - - - +
78A ALA* 1.3 61.0 + - - +
80A ARG* 3.2 31.8 + - - +
81A GLU* 3.3 12.8 + - - +
311A LEU* 3.9 26.4 - - + +
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Residues in contact with ALA 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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75A GLY* 3.4 10.5 + - - +
76A VAL 3.3 0.4 - - - -
77A GLU* 1.3 74.8 - - - +
79A ALA* 1.3 68.3 + - - +
80A ARG 3.0 1.8 - - - -
81A GLU* 3.0 10.2 + - - +
82A ARG* 3.0 37.8 + - + +
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Residues in contact with ALA 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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75A GLY 2.9 19.7 + - - +
76A VAL 3.8 3.1 - - - +
78A ALA* 1.3 74.2 - - - +
80A ARG* 1.3 64.5 + - - +
82A ARG* 3.1 32.1 + - - +
83A MET* 3.1 21.0 + - - +
89A ILE* 4.9 2.3 - - - +
365A LYS* 6.0 0.9 - - - +
498A PHE* 4.0 7.3 - - + -
502A VAL* 3.8 32.8 - - + -
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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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76A VAL* 3.0 12.1 + - + +
77A GLU* 3.2 30.7 + - - +
78A ALA 3.0 0.2 - - - -
79A ALA* 1.3 80.8 - - - +
81A GLU* 1.3 72.7 + - - +
83A MET* 3.1 14.4 + - - +
84A PHE* 3.2 20.3 + - + -
306A PHE* 3.1 55.8 + - + -
307A ARG* 3.2 32.4 + - - +
309A THR 4.2 4.9 + - - -
311A LEU* 3.7 26.5 - - - +
314A ASN* 3.9 7.1 - - - +
317A VAL* 4.7 0.4 - - - +
498A PHE* 3.9 16.1 - - + -
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Residues in contact with GLU 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 GLU 3.3 9.3 + - - +
78A ALA* 3.0 11.7 + - - +
80A ARG* 1.3 81.4 + - - +
82A ARG* 1.3 60.6 + - + +
84A PHE* 3.3 2.4 + - - +
85A ASN* 2.8 47.4 + - - +
307A ARG* 3.0 55.9 + - - +
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Residues in contact with ARG 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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75A GLY* 4.4 5.5 + - - -
78A ALA* 3.0 22.5 + - + +
79A ALA* 3.1 45.2 + - - +
81A GLU* 1.3 78.1 - - + +
83A MET* 1.3 61.4 + - - +
85A ASN* 3.5 0.4 + - - -
86A GLY 3.3 3.5 + - - -
87A GLU* 3.0 64.7 + - - +
89A ILE* 3.7 27.0 - - + +
365A LYS* 4.7 17.4 - - - +
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Residues in contact with MET 83 (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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79A ALA 3.1 11.3 + - - +
80A ARG 3.1 10.1 + - - +
82A ARG* 1.3 78.5 - - - +
84A PHE* 1.3 91.4 + - + +
86A GLY* 3.3 2.1 + - - -
87A GLU 4.6 1.6 + - - +
89A ILE* 3.9 19.2 - - + +
97A VAL* 3.5 28.2 + - - +
98A LEU* 3.2 22.5 - - - +
99A HIS* 4.2 17.3 - - - -
100A VAL* 4.3 8.7 - - + -
306A PHE* 4.2 8.5 - - + -
495A HIS* 3.7 27.4 - - + +
498A PHE* 4.4 25.1 - - + -
509A PHE* 4.9 0.2 - - - -
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Residues in contact with PHE 84 (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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80A ARG* 3.2 30.5 + - + +
81A GLU 4.1 2.5 - - - +
83A MET* 1.3 100.6 - - + +
85A ASN* 1.3 62.1 + - - +
86A GLY 3.2 0.2 - - - -
98A LEU* 4.2 0.3 - - - +
100A VAL* 3.8 38.1 - - + -
110A ILE* 3.2 29.9 - - + +
303A ASP* 3.9 32.1 - - + -
306A PHE* 4.2 5.6 - + - -
307A ARG* 3.2 53.8 + - + +
495A HIS* 4.4 5.8 - + - -
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Residues in contact with ASN 85 (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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81A GLU* 2.8 49.2 + - - +
82A ARG* 4.3 2.6 - - - +
83A MET 3.3 0.2 - - - -
84A PHE* 1.3 72.2 - - - +
86A GLY* 1.3 61.3 + - - +
87A GLU* 3.4 14.3 + - + +
110A ILE* 4.1 4.9 - - - +
111A LEU* 3.4 15.4 + - - +
307A ARG* 3.2 17.7 + - - +
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Residues in contact with GLY 86 (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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83A MET 3.3 9.0 + - - -
84A PHE 3.2 5.6 - - - -
85A ASN* 1.3 80.1 - - - +
87A GLU* 1.3 67.0 + - - +
88A LYS* 3.9 4.0 + - - +
96A ALA* 3.7 12.0 - - - +
98A LEU* 4.0 22.0 - - - -
110A ILE* 4.3 0.7 - - - -
111A LEU 3.7 15.1 - - - +
112A VAL* 3.9 5.9 - - - +
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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