Contacts of the strand formed by residues 93 - 102 (chain G) in PDB entry 3WBR
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 SER 93 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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83G CYS* 3.6 3.0 - - - -
89G SER* 3.5 5.0 - - - -
90G PHE 2.9 28.5 + - - -
91G GLN* 3.4 1.7 + - - +
92G SER* 1.3 81.9 + - - +
94G CYS* 1.3 64.5 + - - +
95G TYR* 3.5 28.7 + - - -
207G LYS* 3.6 20.7 + - - -
208G MET 3.4 10.1 + - - -
209G LYS* 4.4 4.8 - - - +
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Residues in contact with CYS 94 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83G CYS* 2.0 53.2 - - + -
84G PRO* 4.4 5.8 - - - -
87G TRP* 3.5 19.2 - - + -
88G THR 3.1 5.2 - - - +
92G SER 6.0 0.2 - - - -
93G SER* 1.3 75.3 - - - +
95G TYR* 1.3 63.6 + - - +
207G LYS* 3.2 6.9 - - - +
208G MET* 2.8 40.0 + - + +
209G LYS 4.4 15.0 - - - -
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Residues in contact with TYR 95 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86G PRO 4.6 0.3 - - - +
87G TRP* 3.3 8.1 - - - -
88G THR* 2.7 51.0 + - - +
90G PHE* 3.7 28.0 + - + -
91G GLN* 5.5 0.5 + - - -
93G SER* 3.5 32.3 - - - -
94G CYS* 1.3 76.2 - - - +
96G PHE* 1.3 60.7 + - - +
97G ILE* 5.0 12.2 - - + +
119G VAL* 3.9 11.2 - - + -
126G GLU* 2.5 38.1 + - + +
129G PHE* 3.8 20.6 - + + -
130G ILE* 4.0 22.2 - - + -
133G ASN* 6.0 1.3 - - - +
205G ILE* 4.7 3.8 - - + -
206G CYS 3.3 6.7 - - - +
207G LYS* 3.6 20.6 - - + -
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Residues in contact with PHE 96 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86G PRO* 4.3 25.4 - - + -
87G TRP* 3.6 48.0 - + + +
95G TYR* 1.3 74.5 - - - +
97G ILE* 1.3 72.1 + - - +
98G SER* 3.7 28.1 + - - -
114G MET* 3.8 30.3 - - + -
205G ILE* 3.3 5.2 - - - +
206G CYS* 2.8 40.6 + - + -
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Residues in contact with ILE 97 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88G THR* 5.9 2.7 - - - +
95G TYR* 5.0 7.6 - - + -
96G PHE* 1.3 93.0 - - - +
98G SER* 1.3 63.2 + - - +
99G THR* 3.7 8.6 + - + +
130G ILE* 5.5 1.3 - - + +
133G ASN* 4.0 30.3 - - + +
134G LEU* 4.1 15.0 - - + -
135G LYS* 4.0 14.4 - - - +
140G TYR* 3.4 35.9 - - + +
204G SER 3.7 2.0 - - - -
205G ILE* 4.0 18.4 - - + -
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Residues in contact with SER 98 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96G PHE* 3.7 22.0 + - - -
97G ILE* 1.3 75.6 - - - +
99G THR* 1.3 58.4 + - - +
100G GLY* 3.5 12.6 + - - +
110G ASN* 5.2 9.6 + - - +
114G MET* 6.0 0.7 - - - -
140G TYR* 4.9 0.3 - - - -
203G LYS* 3.2 9.9 - - - +
204G SER* 2.8 50.6 + - - +
206G CYS* 5.3 4.5 - - - -
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Residues in contact with THR 99 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137A ASN* 4.5 8.8 + - - +
203A LYS* 4.6 5.7 + - - -
97G ILE* 3.7 8.4 + - + +
98G SER* 1.3 69.6 + - - +
100G GLY* 1.3 64.3 + - - +
101G MET* 3.8 2.4 + - - +
135G LYS* 4.4 22.7 - - - +
203G LYS* 3.3 30.3 - - - +
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Residues in contact with GLY 100 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137A ASN* 3.8 23.3 - - - +
98G SER* 3.4 13.1 + - - +
99G THR* 1.3 79.1 + - - +
101G MET* 1.3 62.4 + - - -
102G GLN* 4.0 6.5 + - - +
202G GLN 3.5 1.4 - - - +
203G LYS* 3.2 20.8 - - - -
204G SER* 5.0 1.0 + - - -
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Residues in contact with MET 101 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101A MET* 3.6 19.5 - - + +
136A ARG 5.0 0.3 - - - +
137A ASN 2.7 23.1 + - - +
138A SER* 4.0 8.0 - - - -
139A SER* 3.6 35.2 - - - +
202A GLN* 3.6 17.9 - - - +
203A LYS* 4.0 24.0 - - - +
99G THR 4.6 2.2 - - - +
100G GLY* 1.3 72.9 - - - -
102G GLN* 1.3 78.2 + - - +
201G PRO* 3.4 32.5 - - + +
202G GLN 3.2 7.2 - - - -
203G LYS* 4.0 20.2 - - + +
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Residues in contact with GLN 102 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136A ARG 4.1 15.6 + - - -
137A ASN* 4.3 8.1 - - - +
185A PHE 5.6 3.4 + - - -
100G GLY* 4.0 5.5 + - - +
101G MET* 1.3 89.7 + - - +
103G SER* 1.3 71.9 + - - +
106G LYS* 4.0 27.3 + - + +
107G SER* 3.5 8.3 + - - +
110G ASN* 4.2 17.0 - - - +
141G PHE* 3.3 3.8 - - - -
201G PRO* 3.6 10.5 - - - -
202G GLN 2.9 25.7 + - - +
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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