Contacts of the helix formed by residues 82 - 94 (chain A) in PDB entry 4G17
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 GLN 82 (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* 5.9 1.2 + - - +
74A GLU* 2.9 7.9 + - - +
80A ALA* 3.8 12.6 - - + +
81A PRO* 1.3 81.6 - - - +
83A LEU* 1.3 61.7 + - - +
84A HIS* 3.7 2.5 - - - -
85A LEU* 3.4 17.9 + - + +
86A GLU* 3.0 30.5 + - - +
185A ASP* 5.6 0.5 - - - +
187A GLY* 3.2 37.8 + - - +
188A LEU* 4.1 17.6 - - - +
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Residues in contact with LEU 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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56A GLU* 5.3 0.9 - - - +
72A LYS* 3.6 49.1 - - + +
73A LEU 4.3 0.2 - - - -
74A GLU* 3.6 33.5 + - + +
82A GLN* 1.3 77.5 - - - +
84A HIS* 1.3 66.0 + - - +
86A GLU* 3.0 13.7 + - - +
87A TYR* 2.9 21.8 + - - +
105A PHE* 3.7 13.5 - - + -
112A ASN* 3.1 36.1 - - + +
113A ALA* 4.0 3.8 - - - +
114A MET* 4.1 14.0 - - + +
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Residues in contact with HIS 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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74A GLU* 4.9 2.2 - - - -
81A PRO* 4.0 28.0 - - + +
82A GLN 4.4 0.2 - - - -
83A LEU* 1.3 80.7 - - - +
85A LEU* 1.3 86.4 + - + +
87A TYR* 3.2 6.9 - - - +
88A ARG* 3.1 26.9 + - + +
105A PHE* 3.4 33.7 - - + -
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Residues in contact with LEU 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 PRO 5.0 4.3 - - - +
82A GLN* 3.7 23.3 - - + +
83A LEU 3.2 0.4 - - - -
84A HIS* 1.3 100.7 - - + +
86A GLU* 1.3 61.4 + - - +
87A TYR 3.1 1.6 - - - -
88A ARG* 3.2 13.1 + - + +
89A PHE* 2.9 49.2 + - + -
187A GLY 5.0 8.7 - - - +
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Residues in contact with GLU 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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72A LYS* 2.8 32.5 + - - +
82A GLN* 3.0 15.7 + - - +
83A LEU* 3.4 16.0 + - - +
85A LEU* 1.3 78.4 - - - +
87A TYR* 1.3 63.2 + - - +
89A PHE* 3.0 15.5 + - - +
90A TYR* 2.9 39.6 + - + -
114A MET* 4.0 12.8 - - + +
185A ASP* 3.2 12.8 + - - -
186A PHE* 2.8 33.1 + - + +
187A GLY* 3.8 12.9 + - - -
401A 0VN 5.0 1.2 + - - -
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Residues in contact with TYR 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 LEU 2.9 11.5 + - - +
84A HIS 3.2 13.9 - - - +
86A GLU* 1.3 77.6 - - - +
88A ARG* 1.3 59.8 + - + +
90A TYR* 3.1 7.4 + - - +
91A LYS* 3.0 58.6 + - + +
102A VAL* 3.6 24.9 - - + -
103A TYR 5.6 0.9 + - - -
104A TYR* 4.3 3.8 - - - -
105A PHE* 3.6 47.9 + + + +
114A MET* 3.7 25.1 - - + -
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Residues in contact with ARG 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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84A HIS* 3.1 17.2 + - - +
85A LEU* 3.2 16.9 + - + +
87A TYR* 1.3 76.3 - - + +
89A PHE* 1.3 68.5 + - + +
91A LYS* 2.9 43.0 + - - +
92A GLN* 3.0 28.4 + - - +
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Residues in contact with PHE 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 LEU* 2.9 39.5 + - + -
86A GLU* 3.0 10.5 + - - +
88A ARG* 1.3 77.0 - - + +
90A TYR* 1.3 58.0 + - - +
92A GLN* 3.1 13.7 + - - +
93A LEU* 2.8 33.7 + - - +
158A LEU* 3.5 38.6 - - + +
186A PHE* 3.5 31.4 - - + -
187A GLY 5.4 1.1 - - - -
189A ALA* 3.5 35.7 - - + -
190A LYS* 4.1 4.5 - - - -
191A GLU* 4.5 8.5 - - + -
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Residues in contact with TYR 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 GLU* 2.9 35.4 + - + -
87A TYR* 3.1 7.6 + - + +
89A PHE* 1.3 77.0 - - - +
91A LYS* 1.3 62.4 + - - +
93A LEU* 3.1 8.8 + - + +
94A GLY* 2.9 22.9 + - - +
99A ILE* 4.0 17.7 - - + -
100A PRO* 3.5 35.6 - - + +
102A VAL* 3.5 30.3 - - + -
114A MET* 3.7 30.1 - - + -
116A LEU* 4.0 9.4 - - + +
184A ILE* 3.9 2.8 - - - +
185A ASP 3.8 13.3 + - - -
186A PHE* 3.7 30.5 - + - -
401A 0VN 4.9 0.7 + - - -
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Residues in contact with LYS 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 TYR* 3.0 43.5 + - + +
88A ARG* 2.9 58.9 + - - +
90A TYR* 1.3 75.2 - - - +
92A GLN* 1.3 62.4 + - - +
94A GLY* 3.3 13.0 + - - -
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Residues in contact with GLN 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 ARG* 3.0 17.6 + - - +
89A PHE* 3.1 17.5 + - - +
91A LYS* 1.3 75.2 - - - +
93A LEU* 1.3 65.8 + - - +
94A GLY* 3.4 0.5 + - - -
156A LYS* 3.1 40.2 + - - +
157A ASN* 4.4 1.8 - - - +
158A LEU* 3.7 25.0 - - + +
191A GLU* 3.3 30.8 + - - +
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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 PHE 2.8 19.2 + - - +
90A TYR* 3.1 11.4 + - + +
92A GLN* 1.3 78.0 - - - +
94A GLY* 1.3 61.3 + - - +
99A ILE* 4.0 21.1 - - + -
152A TYR* 2.6 36.7 + - + -
153A VAL* 4.3 22.2 - - + -
156A LYS* 4.1 24.1 - - + -
158A LEU* 3.8 21.3 - - + -
186A PHE* 3.5 43.1 - - + -
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Residues in contact with GLY 94 (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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90A TYR* 2.9 13.6 + - - +
91A LYS 3.3 9.6 + - - -
92A GLN 3.2 3.6 - - - -
93A LEU* 1.3 89.7 - - - +
95A SER* 1.3 61.9 + - - -
96A GLY 3.4 2.8 + - - -
99A ILE* 4.4 9.0 - - - +
152A TYR* 4.3 0.4 + - - -
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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