Contacts of the strand formed by residues 262 - 266 (chain D) in PDB entry 3FAA
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 262 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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181D ILE* 5.7 0.3 - - - +
184D MET* 3.9 13.0 - - + +
192D GLY* 5.8 4.5 - - - -
198D GLN* 4.2 3.6 - - - -
246D ALA* 4.7 3.8 - - - -
249D TYR* 3.5 47.6 - + + +
250D GLN* 3.6 34.5 - - + -
255D ARG* 3.3 23.7 + - - +
260D LEU 3.2 4.2 + - - -
261D GLY* 1.3 74.7 - - - -
263D ILE* 1.3 65.3 + - - +
264D ALA* 3.2 41.5 - - - -
265D ALA* 3.7 12.8 - - + -
278D LEU* 4.2 19.5 - - + -
279D VAL 4.2 4.3 - - - -
280D SER* 4.5 2.7 - - - -
601D 55F 4.5 7.4 - - + -
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Residues in contact with ILE 263 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177D LEU* 4.0 31.2 - - + -
181D ILE* 4.3 17.5 - - + -
184D MET* 4.4 6.4 - - + +
193D LEU* 3.7 26.8 + - + +
198D GLN* 3.8 6.1 - - - +
201D ILE* 4.4 15.9 - - + -
229D VAL* 4.4 1.3 - - + -
261D GLY 4.1 2.0 - - - +
262D PHE* 1.3 84.3 - - - +
264D ALA* 1.3 63.1 + - + +
279D VAL* 2.7 33.8 + - + +
280D SER* 3.7 26.9 - - - +
281D ASP* 3.8 12.3 - - - +
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Residues in contact with ALA 264 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198D GLN* 3.6 36.6 - - + +
201D ILE* 4.8 5.6 - - + -
202D ALA* 4.9 4.9 - - + -
262D PHE* 3.2 19.3 - - - -
263D ILE* 1.3 85.7 - - + +
265D ALA* 1.3 59.7 - - - +
278D LEU* 3.5 0.9 - - - -
279D VAL* 2.9 39.8 + - + -
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Residues in contact with ALA 265 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195D LEU* 6.0 1.2 - - - +
198D GLN* 2.9 25.4 + - - +
199D ARG* 4.8 1.0 + - - -
202D ALA* 5.3 0.2 - - - -
242D TRP* 4.6 6.7 - - + -
246D ALA* 4.2 12.8 - - + -
250D GLN* 4.5 6.1 - - - +
262D PHE* 3.7 15.5 - - + -
264D ALA* 1.3 75.4 - - - +
266D ASP* 1.3 65.8 + - - +
277D TRP 3.6 7.4 - - - +
278D LEU* 3.9 12.6 - - + -
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Residues in contact with ASP 266 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199D ARG* 3.2 25.3 + - - +
202D ALA* 3.5 28.3 - - + +
203D ARG* 3.2 28.1 + - - -
242D TRP* 3.9 6.0 - - - -
265D ALA* 1.3 77.1 - - - +
267D ASN* 1.3 91.2 + - - +
268D LYS* 4.2 9.5 - - - +
275D GLN 3.7 0.9 - - - +
276D LEU* 3.6 1.7 - - - -
277D TRP* 2.8 42.8 + - + +
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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