Contacts of the strand formed by residues 229 - 237 (chain A) in PDB entry 5BPW
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 SER 229 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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222A GLU* 3.3 29.1 + - - -
223A VAL 3.3 11.8 + - - -
224A SER* 4.2 7.3 - - - +
225A THR* 4.9 0.7 - - - +
228A ALA* 1.3 82.0 + - - +
230A GLU* 1.3 60.9 + - - +
231A VAL* 4.3 2.5 + - - +
557A TYR* 3.8 2.4 - - - +
558A ARG* 3.2 6.5 - - - -
559A ASP* 3.0 32.1 + - - +
562A SER* 3.9 10.4 + - - -
563A GLU* 3.1 14.7 + - - +
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Residues in contact with GLU 230 (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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221A THR 3.6 1.6 - - - +
222A GLU* 3.3 2.3 - - - -
223A VAL* 2.8 43.9 + - + +
224A SER* 4.9 0.2 - - - +
225A THR* 5.4 2.5 + - - +
229A SER* 1.3 72.4 - - - +
231A VAL* 1.3 65.0 + - - +
232A SER* 3.9 13.4 + - - +
555A PRO* 3.7 13.3 - - - +
557A TYR 3.3 10.8 - - - +
558A ARG* 3.5 32.2 + - + +
692A ARG* 3.2 26.4 + - - -
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Residues in contact with VAL 231 (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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206A LEU* 4.0 8.1 - - + -
220A VAL* 3.6 27.1 - - + -
221A THR 3.3 3.8 - - - +
222A GLU* 3.9 27.8 - - + -
229A SER* 5.1 2.2 - - - +
230A GLU* 1.3 79.8 - - - +
232A SER* 1.3 66.4 + - - +
556A LEU* 2.9 28.5 + - + +
557A TYR* 2.9 60.5 + - + +
568A ARG* 6.1 0.7 - - - +
573A PRO* 4.5 1.3 - - + -
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Residues in contact with SER 232 (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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219A VAL 3.8 0.3 - - - +
220A VAL* 3.3 4.0 - - - -
221A THR* 2.9 34.7 + - - +
230A GLU* 3.9 12.4 + - - +
231A VAL* 1.3 75.1 + - - +
233A TYR* 1.3 61.8 + - - +
234A PHE* 4.1 22.9 - - - -
553A CYS* 4.8 3.5 - - - -
554A ILE 3.8 4.9 - - - -
555A PRO* 3.2 28.3 - - - +
556A LEU* 4.0 7.2 - - - +
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Residues in contact with TYR 233 (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 SER* 3.5 32.6 - - - -
219A VAL 3.4 8.7 - - - -
220A VAL* 4.2 7.4 - - + -
232A SER* 1.3 74.1 - - - +
234A PHE* 1.3 68.2 + - - +
235A GLN* 3.2 35.7 + - + +
552A ILE* 4.6 1.1 - - + -
553A CYS* 3.5 5.2 - - - -
554A ILE* 2.9 71.0 + - + +
556A LEU* 4.0 5.3 - - + +
575A LEU* 4.0 11.9 - - + -
584A HIS* 3.9 14.0 - - + +
586A LEU* 3.9 32.1 - - + -
601A LEU* 4.3 14.1 - - + -
603A ARG* 4.0 10.1 - - + +
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Residues in contact with PHE 234 (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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201A ILE* 6.0 5.4 - - + -
202A ALA* 6.2 2.2 - - + -
217A LEU 3.7 0.7 - - - +
218A SER* 3.2 6.1 - - - -
219A VAL* 2.8 47.9 + - + +
221A THR* 3.4 34.8 - - + -
232A SER* 4.1 13.9 - - - -
233A TYR* 1.3 80.9 - - - +
235A GLN* 1.3 60.2 + - - +
236A LEU* 3.9 12.1 + - + -
551A ALA* 4.8 11.9 - - + -
552A ILE 3.2 13.7 - - - -
553A CYS* 3.4 31.0 - - + -
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Residues in contact with GLN 235 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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216A SER* 3.1 34.2 + - - +
217A LEU 3.4 6.7 - - - +
233A TYR* 3.2 28.3 + - + +
234A PHE* 1.3 75.1 - - - +
236A LEU* 1.3 59.6 + - - +
237A GLU 4.1 0.3 + - - -
551A ALA* 3.4 3.3 - - - -
552A ILE* 2.9 40.0 + - + +
584A HIS* 4.4 4.7 - - + -
603A ARG* 2.9 32.2 + - - +
604A HIS 3.3 20.2 + - - -
605A THR 3.4 4.9 + - - -
607A ILE* 3.6 21.8 - - + +
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Residues in contact with LEU 236 (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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185A ILE* 5.9 0.2 - - + -
198A VAL* 3.8 26.0 - - + -
201A ILE* 4.8 14.1 - - + -
216A SER* 3.2 6.8 - - - -
217A LEU* 2.8 57.0 + - + +
219A VAL* 3.7 28.9 - - + -
234A PHE* 4.2 16.2 - - + -
235A GLN* 1.3 73.0 - - - +
237A GLU* 1.3 63.0 + - - +
238A THR* 5.4 0.7 - - + -
548A MET* 3.7 21.3 - - + +
550A GLN 3.3 12.1 - - - +
551A ALA* 4.7 8.3 - - + -
607A ILE* 5.0 0.9 - - - -
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Residues in contact with GLU 237 (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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215A LYS 4.3 0.4 - - - +
235A GLN 4.1 1.0 + - - -
236A LEU* 1.3 72.2 - - - +
238A THR* 1.3 65.0 + - - +
239A ASN* 3.4 35.4 + - + +
547A SER 4.0 0.3 - - - +
548A MET* 3.4 16.8 - - - -
550A GLN* 3.2 46.8 + - + +
607A ILE* 3.4 39.3 - - + +
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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