Contacts of the strand formed by residues 239 - 243 (chain A) in PDB entry 2BBV
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 239 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173A VAL* 5.3 1.3 - - + -
174A GLY* 3.3 4.0 - - - -
175A ILE* 2.8 55.3 + - + +
176A TYR* 4.9 1.6 - - - -
188A ILE* 4.0 18.2 - - + -
190A VAL* 4.1 13.0 - - + -
231A PHE* 3.4 34.5 - - + -
238A GLY* 1.3 73.6 - - - +
240A PHE* 1.3 65.4 + - - +
241A SER* 5.1 1.3 - - - +
299A ILE* 4.6 7.9 - - + -
357A ALA* 3.7 13.9 - - + -
358A VAL 3.3 11.9 - - - +
360A ALA* 3.8 8.5 - - - +
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Residues in contact with PHE 240 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A PHE 3.5 9.6 - - - -
72A ALA* 4.9 0.2 - - - -
73A PRO* 3.6 7.9 - - + -
74A PRO* 3.4 31.4 - - + -
172A ASN* 3.3 26.5 - - + -
173A VAL 3.3 13.7 - - - -
174A GLY* 4.6 0.2 - - - -
176A TYR* 4.1 8.1 - - + +
239A VAL* 1.3 75.2 - - - +
241A SER* 1.3 61.0 + - - +
242A GLN* 3.0 30.9 - - - +
316A TRP* 3.7 17.0 - + - -
357A ALA* 3.6 1.7 - - - -
358A VAL* 2.9 39.5 + - + +
359A ILE 5.0 1.3 - - - +
360A ALA* 5.0 1.8 - - - -
363A ASN* 3.8 24.0 - - + -
366D MET* 4.1 12.8 - - + -
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Residues in contact with SER 241 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172A ASN* 3.3 5.4 + - - +
173A VAL* 2.8 46.5 + - - +
190A VAL* 4.0 5.6 - - - +
192A LYS* 3.6 11.8 - - - -
239A VAL* 5.2 2.2 - - - -
240A PHE* 1.3 79.5 - - - +
242A GLN* 1.3 74.0 + - - +
297A ILE* 3.9 13.8 - - - +
356A VAL 2.8 25.6 + - - -
357A ALA* 3.8 9.1 - - - +
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Residues in contact with GLN 242 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70A ALA 4.0 5.2 - - - +
71A PHE* 2.8 57.8 + - + +
171A MET 3.7 4.5 - - - +
172A ASN* 2.8 25.6 - - - +
192A LYS* 2.9 27.6 + - - +
240A PHE* 3.0 21.8 - - - +
241A SER* 1.3 76.6 + - - +
243A SER* 1.3 62.1 + - - +
244A VAL* 5.8 0.4 - - + -
297A ILE* 3.5 5.2 - - - -
354A LEU* 4.5 8.5 - - + +
355A PRO 4.8 9.9 - - - +
356A VAL 5.2 1.7 - - - +
357A ALA* 5.6 1.0 - - - -
366D MET* 4.3 17.1 - - - +
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Residues in contact with SER 243 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70A ALA 4.6 6.2 - - - +
170A SER* 5.4 1.4 - - - -
171A MET* 3.0 35.1 + - - +
192A LYS* 4.7 4.8 - - - +
242A GLN* 1.3 81.0 - - - +
244A VAL* 1.3 74.9 + - - +
294A MET* 3.4 12.4 - - - +
295A ASP* 2.9 43.7 + - - +
297A ILE* 3.8 9.6 - - - -
347A TYR* 4.7 0.9 + - - -
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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