Contacts of the strand formed by residues 202 - 209 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101B MET* 3.6 6.8 - - - +
200B VAL* 3.5 13.7 - - - +
201B PRO* 2.9 23.9 - - - +
202B GLN* 3.3 2.8 - - - +
100C GLY 3.5 0.9 - - - +
101C MET* 3.2 6.5 - - - +
102C GLN 2.9 28.3 + - - +
107C SER* 4.2 3.8 + - - -
139C SER* 2.7 36.7 + - - +
141C PHE* 3.6 31.0 - - + +
182C ILE* 3.4 24.2 - - + +
196C ILE* 4.0 3.4 - - + -
200C VAL 3.3 2.9 + - - +
201C PRO* 1.3 87.6 - - - +
203C LYS* 1.3 71.5 + - - +
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Residues in contact with LYS 203 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99B THR 4.8 5.3 + - - -
101B MET* 3.9 21.7 - - - +
203B LYS* 4.4 22.8 - - - +
98C SER 3.3 7.6 - - - +
99C THR* 3.4 39.2 - - - +
100C GLY 3.4 8.5 - - - +
101C MET* 4.1 5.2 - - + -
135C LYS* 4.0 11.3 - - - +
137C ASN* 5.2 1.2 + - - +
138C SER* 3.0 30.0 + - - +
139C SER 3.1 12.4 + - - +
140C TYR* 3.1 17.4 - - + -
141C PHE* 2.8 22.2 + - - +
202C GLN* 1.3 78.4 - - - +
204C SER* 1.3 65.2 + - - +
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Residues in contact with SER 204 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97C ILE* 3.7 3.1 - - - -
98C SER* 2.8 48.4 + - - +
100C GLY 5.1 1.2 + - - -
107C SER* 3.6 24.1 + - - -
110C ASN* 5.9 0.7 - - - +
111C CYS* 5.0 2.9 - - - -
118C LEU* 3.6 24.0 - - - +
140C TYR* 3.9 4.2 - - - -
141C PHE* 3.8 9.6 - - - +
202C GLN 5.0 0.2 + - - -
203C LYS* 1.3 80.5 - - - +
205C ILE* 1.3 64.8 + - - +
206C CYS 4.3 0.2 - - - -
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Residues in contact with ILE 205 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95C TYR* 4.7 9.4 - - + -
96C PHE 3.4 4.3 - - - +
97C ILE* 3.8 24.2 - - + -
111C CYS* 4.4 0.2 - - - -
118C LEU* 3.4 8.0 - - - +
119C VAL* 2.8 50.7 + - + +
130C ILE* 4.0 16.4 - - + -
134C LEU* 3.7 17.0 - - + -
140C TYR* 3.7 28.3 - - + -
141C PHE 3.5 4.6 + - - +
142C LEU* 4.5 1.6 - - + -
183C ILE* 3.8 17.3 - - + -
204C SER* 1.3 81.0 - - - +
206C CYS* 1.3 71.4 + - - +
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Residues in contact with CYS 206 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87C TRP* 4.0 20.2 - - + -
95C TYR* 3.3 7.3 - - - +
96C PHE* 2.7 37.6 + - + +
98C SER* 5.2 4.0 - - - -
110C ASN* 5.8 0.7 - - - -
111C CYS* 2.1 53.8 - - + -
114C MET* 4.0 17.0 - - - -
116C ALA* 4.1 1.1 - - + -
117C ASP 3.2 6.7 - - - +
204C SER* 5.1 5.2 - - - -
205C ILE* 1.3 78.3 - - - +
207C LYS* 1.3 62.9 + - - +
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Residues in contact with LYS 207 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87C TRP* 4.3 0.2 - - - -
93C SER* 3.6 19.0 + - - -
94C CYS 3.2 11.4 - - - +
95C TYR* 3.6 13.7 - - + -
116C ALA* 3.3 3.3 - - - +
117C ASP* 2.8 34.6 + - - +
118C LEU 5.2 0.4 - - - +
119C VAL* 3.9 19.3 - - + -
120C VAL* 2.8 29.5 + - - +
122C ASN* 3.4 19.6 - - - +
126C GLU* 2.7 30.0 + - - +
206C CYS* 1.3 77.0 - - - +
208C MET* 1.3 69.2 + - - +
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Residues in contact with MET 208 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84C PRO* 3.2 37.5 - - + -
87C TRP* 3.5 39.7 - - + +
93C SER* 3.4 4.7 - - - -
94C CYS* 2.7 39.4 + - + -
114C MET 4.2 11.2 - - - +
115C GLY* 3.7 28.3 - - - +
116C ALA* 3.8 2.5 - - + -
207C LYS* 1.3 79.2 - - - +
209C LYS* 1.3 69.0 + - - +
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Residues in contact with LYS 209 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92C SER* 2.9 40.5 + - - +
93C SER* 4.4 5.4 - - - +
94C CYS* 4.7 0.6 - - - -
208C MET* 1.3 86.5 - - - +
210C LYS* 1.3 72.0 + - - +
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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