Contacts of the helix formed by residues 78 - 93 (chain A) in PDB entry 6GES
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 HIS 78 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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74A SER 6.1 0.7 - - - -
75A PRO 3.0 9.1 + - - +
76A PHE 3.3 0.4 - - - -
77A GLU* 1.3 103.0 + - + +
79A GLN* 1.3 67.2 + - - +
80A THR* 4.3 6.1 - - - +
81A TYR* 3.2 42.6 + + + +
82A CYS* 3.0 23.2 + - - -
357A LYS* 4.3 1.6 - - - +
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Residues in contact with GLN 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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78A HIS* 1.3 71.7 - - - +
80A THR* 1.3 70.4 + - + +
82A CYS* 3.1 3.7 + - - +
83A GLN* 2.4 52.6 + - - +
353A ASP 3.0 17.9 + - - +
354A ASP* 4.1 1.2 - - - +
355A LEU 2.6 31.4 + - - +
356A PRO* 4.4 1.6 - - + -
357A LYS* 3.8 30.9 - - + +
360A LEU* 3.7 10.1 - - + +
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Residues in contact with THR 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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78A HIS* 4.3 6.3 - - - +
79A GLN* 1.3 88.0 - - + +
81A TYR* 1.3 78.2 + - - +
83A GLN* 3.3 14.2 + - - +
84A ARG* 3.2 47.2 + - - +
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Residues in contact with TYR 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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52A ALA* 4.4 15.9 + - + +
53A TYR* 3.4 55.4 + + + -
74A SER 4.9 1.3 - - - -
75A PRO* 3.6 26.2 - - + +
78A HIS* 3.2 37.5 + + + +
80A THR* 1.3 93.6 + - - +
82A CYS* 1.3 61.4 + - - +
84A ARG* 3.3 15.5 + - - +
85A THR* 2.9 28.9 + - - -
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Residues in contact with CYS 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 PRO* 3.4 23.6 - - - -
76A PHE* 3.6 30.7 - - - -
78A HIS 3.0 11.2 + - - -
79A GLN* 3.1 9.6 + - - +
81A TYR* 1.3 75.2 - - - +
83A GLN* 1.3 64.7 + - - +
85A THR* 3.3 0.8 + - - -
86A LEU* 3.0 26.0 + - - +
357A LYS* 4.0 21.1 - - + -
360A LEU* 3.7 23.4 - - + +
361A LYS* 5.1 0.7 - - - -
364A ILE* 3.8 9.0 - - + +
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Residues in contact with GLN 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 GLN* 2.4 40.1 + - - +
80A THR* 3.4 19.5 + - - +
82A CYS* 1.3 77.5 - - - +
84A ARG* 1.3 63.5 + - + +
86A LEU* 3.6 2.8 + - - +
87A ARG* 3.0 31.9 + - - +
352A LEU 4.7 1.8 - - - +
353A ASP* 2.8 48.1 + - - +
360A LEU* 3.7 19.9 - - + +
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Residues in contact with ARG 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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53A TYR* 3.3 27.4 - - - +
80A THR* 3.2 37.0 + - - +
81A TYR* 3.8 16.5 - - - +
82A CYS 3.2 0.2 - - - -
83A GLN* 1.3 81.3 - - + +
85A THR* 1.3 61.3 + - - +
87A ARG* 3.7 1.4 - - - +
88A GLU* 2.9 31.2 + - - +
186A GLY* 3.2 31.7 - - - +
187A LEU* 3.5 14.7 - - + +
205A VAL* 3.5 40.2 - - - +
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Residues in contact with THR 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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53A TYR* 3.7 4.3 - - - -
73A ILE* 3.5 35.1 - - + +
75A PRO* 3.4 20.4 - - + +
81A TYR 2.9 17.6 + - - -
82A CYS 3.9 3.4 - - - -
84A ARG* 1.3 78.3 - - - +
86A LEU* 1.3 62.6 + - - +
88A GLU* 3.4 4.0 + - - +
89A ILE* 3.0 48.3 + - + +
118A VAL* 5.2 4.7 - - + -
364A ILE* 4.2 16.4 - - + -
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Residues in contact with LEU 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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82A CYS 3.0 17.0 + - - +
83A GLN* 3.9 3.6 - - - +
85A THR* 1.3 78.0 - - - +
87A ARG* 1.3 59.5 + - - +
89A ILE* 3.4 2.8 + - + -
90A GLN* 2.8 67.9 + - + +
352A LEU* 5.0 9.4 - - + -
360A LEU* 4.0 26.9 - - + +
363A LEU* 3.9 40.2 - - + +
364A ILE* 3.8 25.1 - - + +
367A GLU* 4.1 5.6 - - + -
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Residues in contact with ARG 87 (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 GLN 3.0 20.2 + - - +
84A ARG 3.7 4.5 - - - +
85A THR 3.3 0.2 - - - -
86A LEU* 1.3 79.3 - - - +
88A GLU* 1.3 63.7 + - - +
90A GLN* 4.0 3.6 + - - +
91A ILE* 3.1 38.2 + - + +
185A PHE 3.9 12.6 - - - +
186A GLY 4.3 7.2 - - - +
188A ALA 2.9 35.5 + - - +
189A ARG* 4.0 18.6 - - - +
348A PHE* 3.4 57.4 - - - +
349A ALA 5.2 0.4 + - - -
352A LEU* 3.5 19.0 - - - +
353A ASP* 4.3 16.7 + - - -
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Residues in contact with GLU 88 (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 LYS* 2.9 27.1 + - - +
73A ILE* 4.7 3.8 - - - +
84A ARG 2.9 17.6 + - - +
85A THR* 4.0 4.9 - - - +
87A ARG* 1.3 77.9 - - - +
89A ILE* 1.3 59.0 + - - +
91A ILE* 4.0 0.2 - - - -
92A LEU* 2.9 50.5 + - + +
103A ILE* 5.5 0.4 - - + -
120A ILE* 4.1 18.0 - - + +
122A GLN* 5.5 1.4 + - - -
184A ASP* 3.3 15.7 + - - -
185A PHE* 2.9 43.8 + - - +
186A GLY* 4.1 3.1 - - - +
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Residues in contact with ILE 89 (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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85A THR* 3.0 40.8 + - + +
86A LEU* 3.8 4.3 - - + +
88A GLU* 1.3 77.0 - - - +
90A GLN* 1.3 64.3 + - - +
93A LEU* 3.0 49.3 + - + +
103A ILE* 4.3 6.7 - - + -
106A ILE* 4.2 14.1 - - + -
118A VAL* 4.6 6.5 - - + -
120A ILE* 4.0 24.9 - - + -
364A ILE* 4.2 20.9 - - + -
367A GLU* 4.1 18.6 - - + -
368A THR* 4.4 10.5 - - + -
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Residues in contact with GLN 90 (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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86A LEU* 2.8 51.2 + - + +
87A ARG* 4.1 2.7 + - - +
89A ILE* 1.3 73.9 - - - +
91A ILE* 1.3 63.2 + - - +
94A ARG* 3.0 45.9 + - - +
348A PHE* 3.4 33.1 - - + -
352A LEU* 4.6 4.9 - - - +
363A LEU* 5.5 7.9 - - - +
367A GLU* 3.0 36.3 + - + +
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Residues in contact with ILE 91 (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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87A ARG* 3.1 30.6 + - - +
88A GLU* 4.0 2.9 - - - +
90A GLN* 1.3 76.8 - - - +
92A LEU* 1.3 65.3 + - + +
94A ARG* 3.0 13.9 + - - +
95A PHE* 3.2 48.9 + - + -
162A VAL* 3.9 11.9 - - + -
185A PHE* 4.1 14.6 - - + +
188A ALA* 3.5 32.3 - - + -
189A ARG 5.2 0.2 - - - +
346A PHE* 4.5 11.2 - - + -
348A PHE* 3.8 20.6 - - + -
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Residues in contact with LEU 92 (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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88A GLU* 2.9 47.2 + - + +
91A ILE* 1.3 78.7 - - + +
93A LEU* 1.3 63.1 + - - +
94A ARG 3.2 0.5 + - - -
95A PHE* 3.3 20.2 - - + +
100A VAL* 4.1 8.3 - - + -
101A ILE* 3.7 30.6 - - + +
102A GLY* 5.1 1.6 - - - -
103A ILE* 3.7 29.0 + - + +
120A ILE* 6.1 0.2 - - + -
122A GLN* 4.0 21.1 - - - +
185A PHE* 3.6 34.1 - - + -
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Residues in contact with LEU 93 (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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89A ILE* 3.0 37.6 + - + +
90A GLN 4.2 3.6 - - - +
92A LEU* 1.3 77.8 - - - +
94A ARG* 1.3 64.1 + - - +
95A PHE 4.6 1.7 - - - +
103A ILE* 3.9 28.9 - - + +
106A ILE* 4.3 2.2 - - + -
367A GLU* 3.7 27.8 - - - +
370A ARG* 3.7 31.5 + - - +
371A PHE* 3.7 29.2 - - + -
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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