Contacts of the strand formed by residues 367 - 371 (chain A) in PDB entry 2BS3
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 MET 367 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225A ASN* 3.5 37.7 - - + +
226A THR* 4.0 8.5 - - - +
227A THR 4.8 0.2 - - - +
256A PHE* 3.1 10.7 - - - -
257A HIS* 2.8 32.8 + - - +
260A PRO* 4.0 11.8 - - + +
261A LEU 3.7 18.8 - - - +
262A PHE* 3.8 25.8 - - + -
263A PRO 3.7 17.3 - - - +
265A GLY* 3.4 24.9 - - - -
365A LEU* 3.4 13.7 + - + +
366A PRO* 1.3 80.9 - - - +
368A GLN* 1.3 68.1 + - - +
369A HIS* 4.0 0.7 - - - +
475A ASP* 5.9 0.9 - - - -
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Residues in contact with GLN 368 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219A TYR* 5.8 0.2 - - - -
220A GLY* 3.2 21.3 - - - -
223A TYR* 3.7 26.9 - - + -
225A ASN 3.3 15.5 + - - +
226A THR* 2.6 29.6 + - - -
227A THR* 3.0 26.5 + - - +
228A ASN* 3.5 6.6 + - - +
254A VAL* 3.4 22.9 - - + +
255A GLN 3.8 2.0 - - - -
256A PHE* 3.3 18.8 - - + -
367A MET* 1.3 73.8 - - - +
369A HIS* 1.3 66.4 + - - +
370A TYR* 3.4 34.8 + - - +
371A SER* 3.7 7.9 + - - -
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Residues in contact with HIS 369 (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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227A THR* 2.7 24.6 + - + +
228A ASN* 3.0 19.4 + - - -
255A GLN* 2.7 15.8 + - - +
256A PHE 4.1 0.7 - - - -
257A HIS* 3.8 22.0 - - + +
267A LEU* 3.5 18.1 - - + +
368A GLN* 1.3 83.3 + - - +
370A TYR* 1.3 64.8 + - + +
393A GLU* 4.3 2.8 - - - +
404A ARG* 4.1 6.2 + - - -
1656A FAD 3.6 35.5 - + - +
1657A CIT 2.6 57.3 + - - -
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Residues in contact with TYR 370 (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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254A VAL* 3.8 1.6 - - - -
255A GLN* 2.9 45.1 + - + +
368A GLN* 3.5 9.3 + - - -
369A HIS* 1.3 87.3 - - + +
371A SER* 1.3 77.5 + - - +
372A MET* 3.7 22.8 + - - -
393A GLU* 3.4 33.8 - - + -
400A HIS* 3.1 23.9 + + - -
404A ARG* 3.8 27.4 - - + +
409A SER* 3.2 18.2 + - - -
412A GLU* 3.1 11.3 + - - -
1656A FAD 3.0 34.5 - - - -
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Residues in contact with SER 371 (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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218A GLY* 3.7 7.4 - - - -
219A TYR* 3.2 54.3 + - - -
228A ASN* 5.1 0.2 + - - -
253A ALA 4.4 2.5 - - - -
254A VAL* 5.1 1.6 - - - +
368A GLN* 3.7 13.5 + - - -
370A TYR* 1.3 76.8 - - - +
372A MET* 1.3 53.8 + - - +
373A GLY 3.2 2.2 - - - +
393A GLU* 2.8 24.5 + - - +
1658A NA 2.4 27.5 - - - -
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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