Contacts of the strand formed by residues 202 - 208 (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 GLN 202 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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101A MET* 3.5 6.9 - - - +
200A VAL* 3.8 4.2 - - - +
201A PRO* 3.0 23.3 - - - +
202A GLN* 3.5 2.6 - - - +
100G GLY 3.5 0.9 - - - +
101G MET* 3.6 9.0 - - - -
102G GLN 2.9 28.6 + - - +
107G SER* 4.2 3.5 + - - -
139G SER* 2.7 37.6 + - - +
141G PHE* 3.6 28.9 - - + +
182G ILE* 3.5 26.0 - - + +
196G ILE* 3.9 8.7 - - + -
200G VAL 3.3 3.3 + - - +
201G PRO* 1.3 88.3 - - - +
203G LYS* 1.3 72.2 + - - +
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Residues in contact with LYS 203 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99A THR 4.8 4.9 + - - -
101A MET* 4.0 16.5 - - - +
203A LYS* 4.2 22.2 - - - +
98G SER 3.2 7.2 - - - +
99G THR* 3.3 38.5 - - - +
100G GLY 3.2 10.3 - - - +
101G MET* 4.0 8.9 - - + +
135G LYS* 4.0 11.9 - - - +
137G ASN* 6.0 0.2 - - - -
138G SER* 2.9 33.1 + - - +
139G SER 3.3 11.4 + - - +
140G TYR* 3.7 17.0 - - + -
141G PHE* 2.9 20.8 + - - +
202G GLN* 1.3 80.7 - - - +
204G SER* 1.3 62.6 + - - +
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Residues in contact with SER 204 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97G ILE* 3.7 1.0 - - - -
98G SER* 2.8 48.4 + - - +
100G GLY 5.0 1.0 + - - -
107G SER* 3.8 23.0 + - - -
110G ASN* 5.9 1.4 - - - +
111G CYS* 5.1 3.5 - - - -
118G LEU* 3.6 23.0 - - - +
140G TYR* 3.9 4.6 - - - -
141G PHE* 3.9 9.6 - - - +
203G LYS* 1.3 80.6 - - - +
205G ILE* 1.3 65.0 + - - +
206G CYS* 4.3 0.6 - - - -
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Residues in contact with ILE 205 (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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95G TYR* 4.7 6.1 - - + -
96G PHE 3.3 8.7 - - - +
97G ILE* 4.0 14.8 - - + -
118G LEU* 3.3 9.7 - - - +
119G VAL* 2.8 58.3 + - + +
130G ILE* 3.9 17.0 - - + -
134G LEU* 3.7 29.2 - - + -
140G TYR* 3.7 22.0 - - + -
141G PHE 3.5 7.6 + - - +
142G LEU* 4.5 0.2 - - + -
183G ILE* 3.8 16.6 - - + -
204G SER* 1.3 80.4 - - - +
206G CYS* 1.3 64.7 + - - +
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Residues in contact with CYS 206 (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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87G TRP* 3.9 20.0 - - + -
95G TYR* 3.3 5.2 - - - +
96G PHE* 2.8 38.7 + - + +
98G SER* 5.3 2.9 - - - -
110G ASN* 5.8 0.9 - - - -
111G CYS* 2.0 54.1 - - + -
114G MET* 3.9 14.1 - - - -
116G ALA* 4.2 1.1 - - + -
117G ASP 3.2 6.1 - - - +
119G VAL 4.5 0.7 - - - -
204G SER* 5.1 5.6 - - - -
205G ILE* 1.3 80.9 - - - +
207G LYS* 1.3 62.4 + - - +
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Residues in contact with LYS 207 (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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87G TRP* 4.4 0.2 - - - -
93G SER* 3.6 16.8 + - - -
94G CYS 3.2 11.9 - - - +
95G TYR* 3.6 15.7 - - + +
116G ALA* 3.3 3.0 - - - +
117G ASP* 2.8 32.9 + - - +
119G VAL* 3.9 18.8 - - + +
120G VAL* 2.9 28.1 + - - +
122G ASN* 3.0 19.4 - - - +
126G GLU* 2.6 30.8 + - - +
206G CYS* 1.3 76.4 - - - +
208G MET* 1.3 68.6 + - - +
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Residues in contact with MET 208 (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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84G PRO* 3.7 33.9 - - + -
87G TRP* 3.9 36.3 - - + +
93G SER* 3.4 5.8 - - - -
94G CYS* 2.8 41.4 + - + +
114G MET 3.8 21.8 - - - +
115G GLY* 3.7 21.3 - - - +
116G ALA* 3.8 2.5 - - + -
207G LYS* 1.3 79.5 - - - +
209G LYS* 1.3 66.2 + - - +
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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