Contacts of the strand formed by residues 200 - 210 (chain B) in PDB entry 3BWC
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 200 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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168B ASN* 3.1 9.3 - - - +
170B TYR 3.3 14.1 - - - +
171B ASP 3.7 18.8 - - - +
173B VAL* 3.6 31.2 - - + +
196B VAL* 3.2 23.6 + - + +
197B LEU* 3.7 6.3 - - - +
198B ARG 3.2 1.8 - - - +
199B ILE* 1.3 79.3 - - - +
201B LYS* 1.3 64.3 + - - +
204B GLY* 4.2 6.1 - - - +
205B ILE 3.8 4.9 - - - +
206B CYS* 4.0 21.8 - - + +
232B PHE* 3.7 25.8 - - + -
257B LYS* 2.7 31.4 + - + -
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Residues in contact with LYS 201 (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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97B GLU* 5.5 4.4 + - - -
98B ARG* 5.0 9.3 - - - +
168B ASN* 3.5 30.5 - - + +
169B THR 3.4 21.3 - - - -
170B TYR 2.8 19.1 + - - +
171B ASP* 3.6 27.6 + - - +
200B LEU* 1.3 77.5 - - - +
202B PRO* 1.4 69.6 - - + +
203B ASP* 3.2 7.4 - - - +
204B GLY* 2.7 24.5 + - - -
257B LYS* 3.6 5.5 - - - +
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Residues in contact with PRO 202 (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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168B ASN* 4.3 14.8 - - - +
201B LYS* 1.4 90.2 - - + +
203B ASP* 1.3 60.4 + - + +
204B GLY 3.5 1.6 + - - -
257B LYS* 3.8 14.7 - - + +
258B LYS* 3.6 26.9 + - + +
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Residues in contact with ASP 203 (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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93B HIS* 3.0 36.1 + - - +
94B PRO* 3.9 27.5 - - + +
171B ASP* 4.5 1.9 - - - +
201B LYS* 4.3 8.7 - - - +
202B PRO* 1.3 79.7 - - + +
204B GLY* 1.3 61.8 + - - +
205B ILE* 4.2 4.3 - - - +
256B SER* 5.7 0.7 - - - -
258B LYS* 4.2 24.5 - - + -
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Residues in contact with GLY 204 (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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93B HIS* 4.0 1.1 - - - -
171B ASP* 3.2 15.0 - - - -
200B LEU* 4.0 16.8 - - - +
201B LYS 2.7 24.9 + - - -
202B PRO 3.3 2.6 + - - -
203B ASP* 1.3 74.9 - - - +
205B ILE* 1.3 62.1 + - - +
256B SER* 3.8 1.0 + - - -
257B LYS* 3.0 26.2 + - - +
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Residues in contact with ILE 205 (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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89B SER* 3.9 24.0 - - - +
92B SER* 4.0 24.5 - - - +
93B HIS* 4.0 11.0 - - + -
171B ASP 3.0 6.9 + - - -
172B VAL* 3.2 15.2 - - + +
173B VAL 3.0 23.2 + - - -
200B LEU* 3.8 4.3 - - - +
203B ASP 4.2 2.9 - - - +
204B GLY* 1.3 75.7 - - - +
206B CYS* 1.3 70.7 + - - +
254B VAL* 3.9 15.9 - - + -
255B CYS 3.4 6.1 - - - +
256B SER* 3.7 31.2 - - - +
261B VAL* 4.7 3.1 - - + -
263B VAL* 4.0 15.9 - - + -
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Residues in contact with CYS 206 (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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173B VAL 3.4 5.8 - - - +
175B ILE* 5.1 2.5 - - + -
193B TYR* 5.0 7.4 - - - -
196B VAL* 4.1 12.3 - - + -
200B LEU* 4.0 9.3 - - + +
204B GLY 4.3 0.2 - - - -
205B ILE* 1.3 76.6 - - - +
207B CYS* 1.3 64.9 + - - +
208B ASN* 5.0 10.1 - - - -
227B ILE* 4.9 3.6 - - - -
232B PHE* 4.0 18.6 - - + -
253B LEU 5.0 0.7 - - - -
254B VAL* 3.5 3.5 - - - -
255B CYS* 2.0 80.0 + - - +
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Residues in contact with CYS 207 (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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85B LEU* 3.7 34.8 - - - -
88B THR* 6.4 0.4 - - - -
89B SER* 3.8 21.1 - - - -
172B VAL* 5.2 0.4 - - + -
173B VAL 2.7 13.0 + - - +
174B ILE* 4.0 13.9 - - + -
175B ILE* 2.6 38.9 + - - +
206B CYS* 1.3 75.1 - - - +
208B ASN* 1.3 56.4 + - - +
252B THR* 3.4 22.7 - - - -
253B LEU 3.4 5.2 - - - -
254B VAL* 4.8 5.8 - - + -
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Residues in contact with ASN 208 (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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85B LEU* 4.7 1.3 - - - -
175B ILE* 3.5 20.2 - - + +
193B TYR* 3.7 21.9 + - - +
206B CYS* 5.0 5.2 - - - -
207B CYS* 1.3 77.4 - - - +
209B GLN* 1.3 72.0 + - - +
210B GLY* 3.6 1.7 + - - -
223B MSE 4.4 5.2 - - - +
227B ILE* 3.3 31.5 - - - +
252B THR* 2.7 25.0 + - - -
253B LEU* 2.9 46.7 + - - +
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Residues in contact with GLN 209 (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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72B GLN* 5.5 0.6 + - - -
81B TYR* 2.9 37.0 + - + +
85B LEU* 4.7 3.0 - - + +
175B ILE 3.3 4.4 + - - +
176B ASP* 3.3 4.0 - - - +
177B THR* 2.9 49.9 + - - +
208B ASN* 1.3 78.1 - - + +
210B GLY* 1.3 64.7 + - - +
211B GLU* 4.5 7.2 + - - +
223B MSE 4.6 4.3 - - - +
250B ILE* 4.2 14.1 - - + +
251B GLY 3.7 5.8 - - - +
252B THR* 4.4 2.2 - - - +
501B SAM 3.9 20.4 + - - +
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Residues in contact with GLY 210 (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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208B ASN* 3.5 10.7 + - - -
209B GLN* 1.3 76.8 + - - +
211B GLU* 1.3 69.6 + - - -
220B ILE* 5.4 0.9 - - - -
223B MSE 4.8 6.3 - - - -
237B TYR* 4.4 7.6 - - - -
250B ILE* 3.4 17.5 - - - +
251B GLY 2.8 24.9 + - - +
252B THR* 3.7 1.8 - - - +
253B LEU* 4.7 7.4 - - - -
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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