Contacts of the strand formed by residues 212 - 216 (chain B) in PDB entry 4DBW
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 VAL 212 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8B VAL* 4.3 12.1 - - + -
9B LYS 4.9 7.2 - - - +
10B LEU* 3.9 20.9 - - + -
11B ASN 6.0 0.2 - - - +
16B MET* 4.5 3.6 - - - -
187B VAL 2.9 20.0 + - - +
188B CYS* 3.0 10.2 - - + +
189B ASN 2.8 27.2 + - - -
206B CYS* 4.8 0.4 - - - -
210B ASP 5.4 2.2 - - - +
211B ILE* 1.3 74.5 - - - +
213B LEU* 1.3 74.9 + - - +
214B VAL* 4.1 7.6 - - + -
264B GLY 5.3 4.7 - - - +
266B VAL* 3.7 26.0 - - + +
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Residues in contact with LEU 213 (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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189B ASN* 3.7 5.8 - - + +
191B VAL* 3.9 30.1 - - + -
193B CYS* 4.0 14.8 - - - -
199B ARG* 4.2 10.8 - - + -
202B LEU* 4.2 11.0 - - + +
203B LEU* 3.6 52.3 - - + +
206B CYS* 4.6 10.1 - - + +
211B ILE 3.7 3.2 + - - -
212B VAL* 1.3 75.9 - - - +
214B VAL* 1.3 66.6 + - - +
264B GLY 5.3 2.4 + - - -
265B VAL* 3.4 25.5 - - + +
266B VAL 3.1 23.2 + - - -
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Residues in contact with VAL 214 (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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16B MET* 4.1 15.3 - - + -
48B HIS* 5.3 2.5 - - + -
113B LEU* 6.0 0.4 - - + -
188B CYS* 4.2 17.5 - - + -
189B ASN 3.1 7.1 + - - -
190B GLN* 3.3 31.2 - - + +
191B VAL 2.8 30.3 + - - +
212B VAL* 4.1 10.3 - - + -
213B LEU* 1.3 79.3 - - - +
215B ALA* 1.3 63.0 + - - +
266B VAL* 3.2 26.5 - - + +
268B LEU* 3.9 25.4 - - + -
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Residues in contact with ALA 215 (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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191B VAL 3.5 5.4 - - - -
193B CYS* 3.4 33.9 - - + +
214B VAL* 1.3 71.2 - - - +
216B TYR* 1.3 59.6 + - - +
218B ALA* 4.4 0.8 - - + +
260B GLN* 4.3 6.5 - - - -
265B VAL* 3.7 18.7 - - + +
266B VAL 2.8 11.1 + - - +
267B VAL* 4.3 10.0 - - + +
268B LEU* 3.0 34.3 + - - +
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Residues in contact with TYR 216 (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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167B ASN* 2.6 30.3 + - - -
190B GLN* 4.0 4.5 - - + +
191B VAL* 3.0 26.1 + - - -
192B GLU* 3.4 37.1 + - + +
193B CYS 3.1 18.7 + - - -
214B VAL 3.7 0.6 + - - -
215B ALA* 1.3 74.0 - - - +
217B SER* 1.3 79.7 + - - +
218B ALA 3.1 2.5 + - - +
268B LEU* 4.3 6.3 - - + -
306B PHE* 4.1 8.3 - + - -
319B TYR* 4.1 1.4 + - - -
401B NAP 3.1 81.0 - + + +
402B 511 3.7 18.2 - - - +
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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