Contacts of the helix formed by residues 80 - 91 (chain B) in PDB entry 5WRV
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 LEU 80 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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45B VAL* 5.4 1.6 - - + -
48B LEU 4.6 0.7 - - - +
49B HIS* 3.9 43.7 - - + +
52B VAL* 3.9 30.1 - - + -
68B ILE* 3.9 16.8 - - + -
75B LEU* 4.1 21.5 - - + -
78B ASN* 2.7 34.4 + - + +
79B SER* 1.3 80.2 - - - +
81B SER* 1.3 60.7 - - - +
82B PHE 3.3 2.9 - - - -
83B GLU* 3.3 19.6 + - - +
84B LYS* 2.9 26.5 + - - +
201B SO4 3.5 2.7 + - - -
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Residues in contact with SER 81 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79B SER* 3.2 8.8 - - - -
80B LEU* 1.3 76.4 - - - +
82B PHE* 1.3 58.5 + - - +
84B LYS* 4.3 2.2 - - - +
85B ALA* 2.8 33.6 + - - +
100B THR* 3.4 20.0 + - - +
103B SER 5.1 0.7 + - - -
104B ALA* 3.7 24.8 - - - -
111B LEU* 4.3 5.6 - - - -
201B SO4 2.7 36.7 + - - -
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Residues in contact with PHE 82 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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594A ALA* 3.5 30.7 - - + -
597A HIS* 3.9 13.7 - - + -
598A VAL* 3.8 24.2 - - + -
80B LEU 3.3 0.6 - - - -
81B SER* 1.3 79.0 - - - +
83B GLU* 1.3 77.1 + - + +
85B ALA* 3.7 2.0 - - - +
86B TYR* 2.8 34.9 + - + +
108B THR* 5.4 0.2 - - - +
110B LYS* 3.4 60.3 - - + -
111B LEU* 3.8 25.2 - - + +
114B LEU* 3.9 18.3 - - + +
201B SO4 4.7 0.4 + - - -
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Residues in contact with GLU 83 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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598A VAL* 5.2 1.8 - - + -
599A ALA 4.6 4.5 + - - +
49B HIS* 2.7 35.7 + - + +
52B VAL* 3.6 30.3 - - + -
53B VAL* 4.2 10.7 - - + +
56B ILE* 3.9 12.6 - - + -
68B ILE* 4.0 4.5 - - + -
80B LEU* 3.3 22.6 + - + +
82B PHE* 1.3 95.3 - - + +
84B LYS* 1.3 66.4 + - - +
86B TYR* 3.3 5.5 + - - +
87B CYS* 2.9 29.1 + - - -
110B LYS* 5.1 5.0 + - - +
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Residues in contact with LYS 84 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65B LEU* 3.7 12.9 - - + +
68B ILE* 3.5 29.3 - - + +
69B ASN* 3.4 22.9 - - - +
79B SER 5.2 2.7 - - - +
80B LEU 2.9 17.9 + - - +
81B SER* 3.7 5.2 - - - +
83B GLU* 1.3 78.1 - - - +
85B ALA* 1.3 62.2 + - - +
87B CYS* 3.3 3.3 + - - +
88B GLU* 2.8 54.2 + - - +
100B THR* 2.8 25.6 + - + +
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Residues in contact with ALA 85 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81B SER 2.8 20.9 + - - +
82B PHE* 3.8 1.3 - - - +
84B LYS* 1.3 73.2 - - - +
86B TYR* 1.3 58.8 + - - +
88B GLU* 3.3 11.6 + - - -
89B TYR* 2.9 30.5 + - - +
97B ALA* 3.5 14.1 - - - +
100B THR* 3.7 7.2 - - + +
101B ILE* 3.6 23.3 - - + -
114B LEU* 3.6 17.5 - - + -
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Residues in contact with TYR 86 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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592A ASP* 2.5 39.7 + - - -
594A ALA* 3.9 15.3 - - + -
595A LEU* 3.3 20.6 - - + +
598A VAL* 4.3 7.9 - - + -
56B ILE* 3.6 34.1 - - + -
61B PHE* 4.2 1.6 - + - -
82B PHE* 2.8 28.4 + + + +
83B GLU* 3.6 9.2 - - - +
85B ALA* 1.3 73.7 - - - +
87B CYS* 1.3 58.7 + - - +
89B TYR* 3.3 13.3 + + - +
90B ARG* 2.9 61.3 + - + +
114B LEU* 3.4 23.7 - - + +
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Residues in contact with CYS 87 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56B ILE* 3.7 18.8 - - - -
61B PHE* 3.6 35.0 - - + +
64B ALA* 3.6 23.1 - - - -
65B LEU* 4.0 17.3 - - + -
68B ILE* 5.3 1.3 - - - -
83B GLU 2.9 20.7 + - - +
84B LYS* 3.3 5.1 + - - +
86B TYR* 1.3 72.1 - - - +
88B GLU* 1.3 60.2 + - - +
90B ARG* 3.2 3.8 + - - +
91B LEU* 2.9 36.4 + - - +
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Residues in contact with GLU 88 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65B LEU* 4.1 18.8 - - + +
69B ASN* 5.5 0.5 + - - -
84B LYS* 2.8 47.4 + - - +
85B ALA* 3.6 6.6 - - - +
86B TYR 3.3 0.2 - - - -
87B CYS* 1.3 74.7 - - - +
89B TYR* 1.3 61.5 + - - +
91B LEU* 3.1 11.6 + - - -
93B ARG* 2.8 52.0 + - + +
96B ASN* 3.2 25.7 - - + +
97B ALA* 3.4 6.7 - - - +
100B THR* 2.7 23.5 + - - -
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Residues in contact with TYR 89 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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590A PHE* 4.9 6.2 - - - -
592A ASP* 4.4 8.5 - - + +
85B ALA 2.9 17.8 + - - +
86B TYR* 3.4 13.7 - + - +
88B GLU* 1.3 77.3 - - - +
90B ARG* 1.3 79.6 + - - +
92B ASN* 3.1 18.9 + - - -
94B ILE* 3.7 20.2 - - + +
97B ALA* 3.8 11.1 - - + +
114B LEU* 3.8 15.0 - - + -
117B GLN* 3.3 44.3 + - + +
118B VAL* 4.0 15.7 - - + -
121B ARG* 3.8 44.0 + - + +
207B GOL 4.2 9.2 + - - -
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Residues in contact with ARG 90 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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592A ASP* 3.8 6.7 + - - -
595A LEU* 4.3 13.3 - - - +
61B PHE* 3.4 53.9 - - + -
86B TYR* 2.9 62.6 + - + +
87B CYS 3.2 3.1 + - - +
89B TYR* 1.3 89.4 - - + +
91B LEU* 1.3 61.2 + - - +
92B ASN* 3.2 3.9 + - - +
207B GOL 4.1 35.2 + - - -
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Residues in contact with LEU 91 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61B PHE* 4.0 21.3 - - + +
62B LYS* 3.8 47.3 - - + +
65B LEU* 4.0 18.6 - - + -
87B CYS 2.9 20.0 + - - +
88B GLU 3.1 4.4 + - - +
90B ARG* 1.3 78.3 - - - +
92B ASN* 1.3 68.6 + - - +
93B ARG* 3.2 40.2 + - - +
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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