Contacts of the helix formed by residues 77 - 85 (chain A) in PDB entry 1WG8
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 77 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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74A ASN* 2.9 22.7 + - + +
76A ARG* 1.3 107.2 + - + +
78A LEU* 1.3 63.6 + - - +
79A LYS 3.4 2.7 - - - -
80A ARG* 3.2 37.0 + - - +
81A HIS* 2.9 47.4 + + + +
218A GLN* 3.6 2.9 - - - -
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Residues in contact with LEU 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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27A VAL* 3.7 28.3 - - + -
29A ALA* 5.3 0.2 - - + -
50A LEU* 4.3 20.6 - - + -
75A PHE 3.1 18.0 + - - +
77A HIS* 1.3 76.9 - - - +
79A LYS* 1.3 63.0 + - - +
81A HIS* 3.3 1.5 + - - +
82A LEU* 2.9 43.7 + - + +
93A ILE* 4.4 4.7 - - + -
215A PHE* 3.9 20.4 - - + -
218A GLN* 3.2 10.1 + - + +
219A ALA* 3.8 33.7 - - + +
222A VAL* 4.2 9.0 - - + -
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Residues in contact with LYS 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 LEU* 1.3 76.1 - - - +
80A ARG* 1.3 64.0 + - - +
82A LEU* 3.8 3.4 - - - +
83A ALA* 3.0 26.3 + - + +
87A VAL 4.9 0.3 - - - +
89A ARG* 5.9 2.0 - - - +
218A GLN* 2.9 32.2 + - + +
221A GLU* 2.7 39.1 + - - +
222A VAL* 4.1 23.6 - - + -
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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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77A HIS* 3.2 49.0 + - + +
79A LYS* 1.3 79.6 - - - +
81A HIS* 1.3 84.2 + - - +
83A ALA* 3.2 8.1 + - + +
84A ALA* 3.1 21.6 + - - +
218A GLN* 4.5 0.6 + - - -
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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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50A LEU* 4.6 13.9 - - + -
71A VAL* 4.5 27.5 - - + +
72A GLN 5.0 1.6 + - - -
73A GLY* 4.4 16.2 - - - -
74A ASN 4.1 10.2 + - - -
77A HIS* 2.9 45.7 + + + +
78A LEU* 4.0 3.6 - - - +
80A ARG* 1.3 102.3 + - - +
82A LEU* 1.3 65.7 + - - +
84A ALA* 3.3 16.0 + - - +
85A LEU* 3.3 18.7 + - - +
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Residues in contact with LEU 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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27A VAL* 3.9 15.0 - - + -
48A ILE* 3.6 40.4 - - + -
50A LEU* 5.8 1.6 - - + -
78A LEU* 2.9 37.8 + - + +
79A LYS* 3.8 3.4 - - - +
81A HIS* 1.3 77.0 - - + +
83A ALA* 1.3 56.3 + - - +
85A LEU* 3.0 11.1 + - - +
86A GLY 3.2 0.2 + - - -
87A VAL* 2.8 47.6 + - + +
90A VAL* 4.0 14.4 - - + -
222A VAL* 3.9 33.9 - - + -
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Residues in contact with ALA 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 LYS* 3.0 20.5 + - + +
80A ARG* 3.4 9.2 - - + +
82A LEU* 1.3 78.2 - - - +
84A ALA* 1.3 55.7 + - - +
86A GLY* 2.9 18.9 + - - -
87A VAL 3.4 11.6 + - - +
88A GLU* 5.8 4.7 - - + -
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Residues in contact with ALA 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* 3.1 13.9 + - - +
81A HIS* 3.6 13.7 - - - +
82A LEU 3.1 0.4 - - - -
83A ALA* 1.3 76.2 - - - +
85A LEU* 1.3 62.5 + - + +
86A GLY 3.2 1.5 + - - -
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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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48A ILE* 3.7 38.1 - - + -
50A LEU* 6.0 0.2 - - + -
69A THR* 4.2 18.8 - - + -
71A VAL* 3.7 19.5 - - + -
81A HIS 3.5 13.5 - - - +
82A LEU* 3.0 11.3 + - - +
84A ALA* 1.3 79.4 - - + +
86A GLY* 1.3 61.3 + - - +
87A VAL* 3.8 12.5 - - + +
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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