Contacts of the helix formed by residues 67 - 83 (chain A) in PDB entry 2GDZ
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 ASP 67 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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64A ASP* 2.9 17.7 + - + +
65A VAL 4.3 0.4 - - - -
66A ALA* 1.3 76.0 - - - +
68A GLN* 1.3 60.2 + - - +
69A GLN* 3.2 10.7 + - - +
70A GLN* 2.8 54.4 + - + +
71A LEU* 2.9 26.2 + - - +
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Residues in contact with GLN 68 (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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65A VAL 5.4 1.8 - - - +
66A ALA 3.5 8.7 + - - +
67A ASP* 1.3 74.1 + - - +
69A GLN* 1.3 57.8 + - - +
71A LEU* 3.2 6.9 + - + +
72A ARG* 2.9 57.8 + - - +
109A VAL* 4.7 11.2 - - + +
113A SER* 3.3 34.8 + - - +
117A LEU* 5.0 1.7 - - - +
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Residues in contact with GLN 69 (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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67A ASP* 3.2 6.9 + - - +
68A GLN* 1.3 76.8 - - - +
70A GLN* 1.3 57.2 + - - +
72A ARG* 2.8 43.4 + - - +
73A ASP* 2.9 60.2 + - - +
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Residues in contact with GLN 70 (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 GLN 4.6 1.4 - - - +
63A CYS* 3.6 16.2 - - - -
64A ASP* 2.9 33.2 + - - +
67A ASP* 2.8 49.1 + - + +
69A GLN* 1.3 76.3 - - - +
71A LEU* 1.3 57.2 + - - +
73A ASP* 3.4 9.0 + - - +
74A THR* 2.8 32.4 + - - -
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Residues in contact with LEU 71 (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 LEU* 6.0 0.2 - - + -
11A THR* 5.0 7.0 - - + -
35A VAL* 5.4 0.9 - - + -
63A CYS* 3.7 18.2 - - - -
65A VAL* 3.7 36.6 - - + +
67A ASP 2.9 15.0 + - - +
68A GLN* 3.2 5.8 + - - +
70A GLN* 1.3 77.0 - - - +
72A ARG* 1.3 62.2 + - - +
74A THR* 3.2 7.8 + - + -
75A PHE* 3.1 46.3 + - + -
110A SER 4.3 4.5 - - - +
113A SER* 4.2 9.0 - - - -
114A GLY* 3.7 32.1 - - - +
117A LEU* 3.7 14.1 - - + -
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Residues in contact with ARG 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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68A GLN* 2.9 44.0 + - + +
69A GLN* 2.8 53.8 + - - +
71A LEU* 1.3 77.2 - - - +
73A ASP* 1.3 61.8 + - - +
75A PHE* 3.3 4.9 + - - +
76A ARG* 3.1 21.9 + - - +
117A LEU* 3.8 33.7 - - + +
121A TYR* 4.5 1.9 + - - -
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Residues in contact with ASP 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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69A GLN* 2.9 46.3 + - - +
70A GLN* 3.6 8.1 - - - +
72A ARG* 1.3 75.7 - - - +
74A THR* 1.3 58.2 + - - +
76A ARG* 3.3 22.2 + - - +
77A LYS* 2.9 53.5 + - - +
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Residues in contact with THR 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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9A LEU* 4.8 4.7 - - + -
35A VAL* 3.7 38.4 - - + -
61A ILE* 3.7 25.0 - - + +
62A GLN 4.4 0.7 + - - -
63A CYS* 3.2 21.0 - - - +
70A GLN 2.8 21.3 + - - -
71A LEU* 3.4 9.6 - - + -
73A ASP* 1.3 73.5 - - - +
75A PHE* 1.3 65.8 + - - +
77A LYS* 3.3 5.7 + - - +
78A VAL* 3.0 31.2 + - + +
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Residues in contact with PHE 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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9A LEU* 4.0 22.9 - - + -
11A THR* 5.8 0.9 - - + -
71A LEU* 3.1 50.9 + - + -
72A ARG* 3.7 6.7 - - - +
74A THR* 1.3 74.9 - - - +
76A ARG* 1.3 64.3 + - - +
78A VAL* 3.2 2.1 + - - +
79A VAL* 3.0 27.9 + - + +
85A LEU* 4.0 23.3 - - + -
88A LEU* 3.6 23.6 - - + -
114A GLY* 3.6 20.6 - - - -
117A LEU* 3.9 18.8 - - + -
118A GLY* 3.6 22.9 - - - -
121A TYR* 3.6 24.7 - + + -
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Residues in contact with ARG 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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72A ARG 3.1 11.7 + - - +
73A ASP* 3.3 21.6 + - - +
75A PHE* 1.3 77.6 - - - +
77A LYS* 1.3 93.1 + - - +
79A VAL* 3.4 1.3 + - - +
80A ASP* 2.9 58.6 + - - +
121A TYR* 3.3 19.9 + - - +
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Residues in contact with LYS 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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59A LEU* 4.5 2.7 - - - +
61A ILE* 4.4 36.3 - - + +
62A GLN 5.9 0.4 + - - -
73A ASP* 2.9 38.1 + - - +
74A THR* 3.8 4.8 + - - +
75A PHE 3.3 0.2 - - - -
76A ARG* 1.3 106.2 - - - +
78A VAL* 1.3 58.5 + - - +
80A ASP* 3.7 6.6 - - - +
81A HIS* 2.9 31.0 + - - +
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Residues in contact with VAL 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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7A VAL* 4.6 5.2 - - + -
9A LEU* 3.9 29.6 - - + -
33A ALA* 3.5 34.5 - - + -
35A VAL* 4.8 0.7 - - + -
59A LEU* 4.5 6.5 - - + -
61A ILE* 4.5 13.7 - - + -
74A THR* 3.0 23.5 + - + +
75A PHE 3.6 4.5 - - - +
77A LYS* 1.3 77.9 - - - +
79A VAL* 1.3 59.1 + - + +
81A HIS* 3.2 2.3 + - - +
82A PHE* 2.9 39.4 + - + +
84A ARG 4.9 0.4 - - - +
85A LEU* 4.6 12.1 - - + -
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Residues in contact with VAL 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 PHE* 3.0 16.5 + - - +
76A ARG 4.1 2.0 - - - +
78A VAL* 1.3 73.7 - - + +
80A ASP* 1.3 63.6 + - - +
83A GLY* 2.7 37.0 + - - +
84A ARG* 4.3 17.7 - - - +
85A LEU* 4.0 27.8 - - + -
121A TYR* 3.6 36.8 - - + -
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Residues in contact with ASP 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 ARG* 2.9 53.1 + - - +
77A LYS* 3.7 7.0 - - - +
79A VAL* 1.3 79.0 - - - +
81A HIS* 1.3 63.4 + - - +
83A GLY* 4.2 2.8 + - - -
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Residues in contact with HIS 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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56A GLN* 4.9 4.4 + - - -
58A THR 4.8 3.8 + - - -
59A LEU* 4.0 33.4 - - + +
77A LYS 2.9 18.3 + - - +
78A VAL 3.2 2.9 + - - +
80A ASP* 1.3 80.8 - - - +
82A PHE* 1.3 99.9 + + - +
83A GLY 3.8 0.2 + - - -
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Residues in contact with PHE 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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7A VAL* 3.7 36.6 - - + +
31A LYS* 3.7 33.1 - - + +
32A VAL 4.0 11.2 - - - -
33A ALA* 3.9 20.9 - - + -
56A GLN 3.8 16.4 - - - -
57A LYS 4.0 8.5 - - - -
58A THR 4.1 0.9 - - - -
59A LEU* 3.9 24.7 - - + -
78A VAL* 2.9 22.5 + - + +
81A HIS* 1.3 108.0 - + + +
83A GLY* 1.3 57.5 + - - +
84A ARG* 3.3 14.5 + - - +
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Residues in contact with GLY 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 VAL* 2.7 25.7 + - - +
80A ASP 4.2 2.4 + - - -
81A HIS 3.4 2.4 + - - -
82A PHE* 1.3 75.2 - - - +
84A ARG* 1.3 61.3 + - - +
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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