Contacts of the strand formed by residues 267 - 271 (chain C) in PDB entry 3R2W
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 PHE 267 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216C TYR* 4.4 6.3 - - - -
265C CYS* 3.3 3.2 + - - +
266C GLU* 1.3 80.2 - - - +
268C VAL* 1.3 69.9 + - - +
269C MET* 4.4 5.1 + - + -
291C LEU* 5.5 0.3 - - - +
321C LEU* 3.6 32.5 - - + -
322C TRP 3.7 14.8 - - - -
323C ILE* 3.7 33.7 - - + -
361C VAL 4.5 8.1 - - - -
362C GLY* 4.9 1.3 - - - -
364C ALA 3.8 19.5 - - - -
365C ILE* 3.7 31.4 - - + -
368C PHE* 3.9 32.3 - + + -
370C ASN 3.9 2.6 + - - -
371C SER* 3.5 7.3 - - - +
372C LEU 3.5 23.0 + - - +
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Residues in contact with VAL 268 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252C ILE* 5.7 3.4 - - + -
255C HIS 5.4 2.0 - - - +
256C LEU* 4.3 25.4 - - + -
265C CYS* 4.5 12.8 - - + -
267C PHE* 1.3 83.8 - - - +
269C MET* 1.3 65.9 + - - +
270C GLU 4.7 0.9 - - - +
321C LEU* 3.3 8.8 - - - +
322C TRP* 3.1 51.4 + - + +
372C LEU* 3.3 25.8 - - + +
374C ILE* 4.1 25.1 - - + -
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Residues in contact with MET 269 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267C PHE* 4.4 8.0 + - + -
268C VAL* 1.3 78.0 - - - +
270C GLU* 1.3 68.9 + - - +
271C VAL* 3.6 4.0 + - - +
284C LEU* 4.0 24.7 - - + -
317C ASN* 4.8 6.1 - - - +
320C ASN 4.0 4.3 - - - +
321C LEU* 4.0 18.2 - - + -
362C GLY* 6.4 0.2 - - - -
365C ILE* 6.1 1.8 - - + -
372C LEU 4.8 0.2 - - - -
373C GLY* 3.3 10.1 - - - -
374C ILE 3.1 21.4 + - - -
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Residues in contact with GLU 270 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237C PHE* 3.9 2.8 - - - -
252C ILE* 4.5 0.2 - - - -
268C VAL* 4.2 2.0 - - + +
269C MET* 1.3 74.0 - - - +
271C VAL* 1.3 62.8 + - - +
317C ASN* 4.7 0.2 - - - -
318C THR* 2.5 34.6 + - - +
319C ASN 4.9 0.2 + - - -
320C ASN* 3.0 46.8 + - - +
321C LEU* 4.9 0.2 - - - +
322C TRP* 3.2 28.3 - - + -
374C ILE* 3.5 15.7 - - + -
376C VAL* 3.5 24.3 - - + +
380C ARG* 2.9 40.9 + - - +
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Residues in contact with VAL 271 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75C ILE* 4.4 13.2 - - + -
269C MET* 4.1 5.6 - - + +
270C GLU* 1.3 82.3 - - - +
272C THR* 1.3 63.7 + - - +
284C LEU* 4.0 26.5 - - + -
315C ILE* 4.3 20.4 - - + -
316C PHE 3.1 21.1 - - - +
317C ASN* 4.5 2.9 - - - -
318C THR* 3.1 4.7 + - - -
373C GLY* 4.7 1.3 - - - -
374C ILE 2.8 32.5 + - - +
375C ASN* 3.3 8.0 - - - +
376C VAL* 2.6 34.4 + - - +
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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