Contacts of the strand formed by residues 208 - 212 (chain B) in PDB entry 3BDW
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 CYS 208 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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140B TRP* 3.6 34.8 - - + -
174B TRP* 3.7 20.5 - - + -
177B VAL 3.8 3.4 - - - -
178B PHE* 4.5 4.5 - - - -
179B ARG 5.7 0.2 - - - -
186B TRP* 3.6 6.7 - - - -
207B ASN* 1.3 81.4 - - - +
209B ALA* 1.3 60.8 + - - +
218B SER* 3.8 2.3 - - - -
219B ALA* 2.9 30.4 + - - +
221B CYS* 2.0 45.5 - - - -
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Residues in contact with ALA 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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174B TRP* 3.0 17.7 - - - -
175B ILE* 3.2 37.0 + - + +
177B VAL* 3.1 33.4 + - + +
186B TRP* 3.7 6.7 - - + -
194B PHE* 5.8 0.4 - - + -
198B ILE* 4.3 13.5 - - + -
208B CYS* 1.3 73.7 - - - +
210B VAL* 1.3 60.7 + - - +
216B LEU* 5.9 0.7 - - + -
217B LYS 3.5 8.3 - - - +
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Residues in contact with VAL 210 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173B SER 3.2 23.1 - - - +
174B TRP* 3.2 25.1 - - + +
175B ILE* 4.3 4.0 - - - +
209B ALA* 1.3 72.6 - - - +
211B LEU* 1.3 58.8 + - - +
212B GLN* 4.5 14.4 - - + +
216B LEU* 3.6 1.9 - - - -
217B LYS* 2.7 55.3 + - + +
219B ALA* 3.1 32.8 - - + -
225B ILE* 3.6 23.8 - - + -
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Residues in contact with LEU 211 (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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155B LEU* 4.6 4.9 - - + -
157B ILE* 3.8 23.1 - - + -
163B MET* 3.2 38.1 - - + +
166B LEU* 4.1 26.9 - - + +
167B SER* 5.4 1.1 - - - +
170B SER 5.9 1.6 - - - +
171B PRO 3.5 1.9 - - - +
172B SER* 3.2 2.6 - - - -
173B SER* 2.6 44.9 + - - +
175B ILE* 4.0 14.1 - - + +
210B VAL* 1.3 70.1 - - - +
212B GLN* 1.3 60.4 + - - +
213B VAL 5.2 0.7 - - - +
214B ASN* 4.4 6.7 - - - +
215B ARG 3.4 24.5 - - - +
216B LEU* 4.2 7.9 - - + +
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Residues in contact with GLN 212 (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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171B PRO 3.2 4.7 - - - +
172B SER* 3.8 22.2 - - - -
199B LYS* 5.2 1.8 + - - +
210B VAL* 3.7 19.9 + - + +
211B LEU* 1.3 76.2 - - - +
213B VAL* 1.3 82.6 - - + +
215B ARG* 2.9 21.2 + - - +
217B LYS* 3.8 37.8 + - + +
225B ILE* 5.0 6.8 - - - +
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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