Contacts of the helix formed by residues 86 - 101 (chain A) in PDB entry 1WS6
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 86 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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84A GLU* 2.9 18.2 + - - +
85A LYS* 1.3 85.0 - - + +
87A PRO* 1.3 73.5 - - - +
88A GLU* 2.9 30.0 + - - +
89A ALA* 2.9 11.2 + - + +
90A VAL* 2.8 22.0 + - - +
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Residues in contact with PRO 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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85A LYS 3.1 11.4 - - - +
86A ASP* 1.3 86.2 - - - +
88A GLU* 1.3 58.6 + - + +
90A VAL* 3.6 9.9 - - + +
91A ARG* 2.9 28.9 + - - +
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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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31A PRO* 5.1 10.9 - - - +
86A ASP* 2.9 18.8 + - - +
87A PRO* 1.3 76.9 - - + +
89A ALA* 1.3 66.9 + - - +
91A ARG* 2.9 20.7 + - - +
92A LEU* 3.0 18.5 + - - +
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Residues in contact with ALA 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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31A PRO* 5.6 8.1 - - + -
65A GLY* 3.7 20.5 - - - +
66A SER 5.0 0.2 - - - +
84A GLU* 3.6 26.5 - - + +
86A ASP* 2.9 17.4 + - + +
88A GLU* 1.3 79.1 - - - +
90A VAL* 1.3 51.2 + - - +
92A LEU* 3.1 12.1 + - - +
93A LEU* 2.7 35.3 + - - +
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Residues in contact with VAL 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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84A GLU* 3.3 35.7 - - + +
85A LYS 4.7 0.7 - - - -
86A ASP 2.8 19.2 + - - +
87A PRO* 3.6 11.9 - - + +
89A ALA* 1.3 75.6 - - - +
91A ARG* 1.3 63.9 + - - +
93A LEU* 3.3 7.0 - - - +
94A LYS* 2.9 50.1 + - - +
106A VAL* 4.2 9.6 - - + -
108A ALA* 4.0 23.3 - - + -
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Residues in contact with ARG 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 PRO 2.9 14.7 + - - +
88A GLU* 2.9 14.8 + - - +
90A VAL* 1.3 78.9 - - - +
92A LEU* 1.3 65.5 + - + +
94A LYS* 3.3 7.6 + - - +
95A GLU* 3.1 40.5 + - + +
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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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29A LYS* 4.3 26.0 - - + +
30A VAL 4.4 1.1 - - - -
31A PRO* 3.1 46.9 - - + -
66A SER* 4.5 5.2 - - - +
88A GLU* 3.0 17.1 + - + +
89A ALA* 3.5 9.0 - - - +
91A ARG* 1.3 77.5 - - + +
93A LEU* 1.3 60.9 + - - +
95A GLU* 3.2 25.1 + - - +
96A ASN* 2.8 35.6 + - - -
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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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64A ALA* 4.8 1.6 - - + -
65A GLY 3.5 16.4 - - - +
66A SER 3.5 18.8 + - - +
67A GLY* 4.3 1.6 - - - +
71A LEU* 4.6 2.9 - - + -
82A LEU* 3.9 36.3 - - + +
84A GLU* 4.7 15.0 - - + -
89A ALA 2.7 20.4 + - - +
90A VAL* 3.3 8.5 - - - +
92A LEU* 1.3 72.7 - - - +
94A LYS* 1.3 57.1 + - - +
96A ASN* 3.1 2.1 + - - +
97A VAL* 2.9 38.6 + - + +
106A VAL* 3.7 30.7 - - + -
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Residues in contact with LYS 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 VAL* 2.9 40.5 + - + +
91A ARG* 3.7 7.0 - - - +
93A LEU* 1.3 73.0 - - - +
95A GLU* 1.3 66.0 + - + +
97A VAL* 3.2 9.8 + - - +
98A ARG* 3.1 26.7 + - - +
106A VAL* 4.1 24.2 - - + -
108A ALA* 5.6 3.6 - - - +
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Residues in contact with GLU 95 (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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29A LYS* 2.9 42.5 + - + +
91A ARG* 3.1 34.4 + - + +
92A LEU* 3.2 18.1 + - - +
94A LYS* 1.3 76.5 - - + +
96A ASN* 1.3 57.8 + - - +
98A ARG* 3.2 10.9 + - - +
99A ARG* 2.9 31.5 + - - +
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Residues in contact with ASN 96 (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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28A LEU* 3.5 14.9 - - + +
29A LYS* 2.7 53.2 + - - +
66A SER* 3.0 24.2 + - - +
71A LEU* 3.6 19.3 - - + -
92A LEU 2.8 17.8 + - - +
93A LEU 3.5 4.9 - - - +
94A LYS 3.1 0.2 - - - -
95A GLU* 1.3 73.7 - - - +
97A VAL* 1.3 63.4 - - - +
98A ARG 3.1 1.8 - - - -
99A ARG* 3.7 10.2 - - - +
100A THR* 3.0 31.2 + - - +
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Residues in contact with VAL 97 (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 LEU* 3.8 21.5 - - + -
82A LEU* 5.9 0.2 - - + -
93A LEU* 2.9 26.2 + - + +
94A LYS* 3.2 11.0 + - - +
96A ASN* 1.3 75.0 - - - +
98A ARG* 1.3 59.6 + - + +
100A THR* 3.2 8.3 + - - -
101A GLY* 2.9 22.0 + - - -
102A LEU 3.3 23.7 + - - +
104A ALA* 4.4 16.8 - - + +
106A VAL* 4.1 17.5 - - + -
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Residues in contact with ARG 98 (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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94A LYS 3.1 16.0 + - - +
95A GLU* 3.2 12.8 - - - +
97A VAL* 1.3 77.7 - - + +
99A ARG* 1.3 66.6 + - + +
101A GLY* 2.9 15.1 + - - -
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Residues in contact with ARG 99 (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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26A VAL* 3.0 27.6 - - + +
27A ALA* 2.6 41.8 + - - +
29A LYS* 3.0 38.6 - - - +
95A GLU 2.9 20.9 + - - +
96A ASN* 3.4 24.0 + - - +
98A ARG* 1.3 73.8 - - + +
100A THR* 1.3 61.4 + - + +
101A GLY 3.5 0.2 + - - -
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Residues in contact with THR 100 (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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18A ILE* 4.3 11.4 - - + -
22A LYS 5.4 0.7 - - - +
23A ALA* 3.9 15.3 - - - +
26A VAL* 3.9 16.3 - - + +
28A LEU* 3.5 28.0 - - + -
71A LEU* 4.4 7.0 - - + +
96A ASN 3.0 20.1 + - - +
97A VAL* 3.2 8.7 + - - -
99A ARG* 1.3 76.6 - - - +
101A GLY* 1.3 64.7 + - - +
102A LEU* 3.1 32.5 + - - +
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Residues in contact with GLY 101 (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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97A VAL 2.9 5.3 + - - -
98A ARG* 2.9 17.2 + - - -
99A ARG 3.2 0.4 - - - -
100A THR* 1.3 78.9 - - - +
102A LEU* 1.3 64.3 + - - +
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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