Contacts of the strand formed by residues 262 - 268 (chain A) in PDB entry 3RS9
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 LEU 262 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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229A LYS* 3.9 32.1 - - + -
233A GLY 3.1 4.5 + - - +
234A LYS* 3.2 33.8 - - + +
235A VAL 2.9 25.3 + - - +
256A LEU* 4.9 1.1 - - - -
260A THR* 3.8 1.2 - - - +
261A GLY* 1.3 80.5 - - - +
263A VAL* 1.3 69.2 + - - +
264A LYS* 4.3 9.6 - - + +
281A GLU 5.7 3.8 - - - +
283A ILE* 3.8 31.6 - - + -
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Residues in contact with VAL 263 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235A VAL* 3.6 9.6 - - + +
237A ILE* 3.9 15.3 - - + -
252A GLY* 3.9 25.8 - - - -
255A SER* 3.5 26.0 - - - -
256A LEU* 3.6 25.6 - - + +
260A THR* 4.2 7.0 - - + -
262A LEU* 1.3 84.5 - - - +
264A LYS* 1.3 65.1 + - - +
265A LEU* 4.1 4.9 - - + -
281A GLU 4.9 2.2 + - - +
282A LEU* 4.1 15.7 - - + +
283A ILE* 3.2 29.2 + - - +
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Residues in contact with LYS 264 (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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235A VAL 2.9 12.2 + - - +
236A LEU* 3.2 18.1 - - + +
237A ILE* 2.8 26.5 + - - +
262A LEU* 5.2 9.6 - - + +
263A VAL* 1.3 76.8 - - - +
265A LEU* 1.3 64.6 + - - +
283A ILE* 3.4 31.2 - - + +
285A VAL* 4.1 20.9 - - + -
305A LEU* 4.2 19.8 + - + +
308A ASP* 5.4 10.8 + - + +
309A VAL* 4.8 14.4 - - + -
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Residues in contact with LEU 265 (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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236A LEU* 4.4 2.0 - - - -
237A ILE* 3.2 22.4 - - + +
248A PRO* 3.6 34.3 - - + +
252A GLY* 3.8 19.7 - - - -
263A VAL* 4.1 4.3 - - + -
264A LYS* 1.3 75.7 - - - +
266A ALA* 1.3 56.1 + - - +
267A VAL* 3.9 12.6 - - + -
275A ALA* 3.5 32.3 - - + -
282A LEU* 4.2 12.1 - - + -
283A ILE 2.8 15.0 + - - +
284A SER* 3.7 10.1 - - - +
285A VAL* 2.8 36.1 + - - +
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Residues in contact with ALA 266 (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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236A LEU* 4.2 6.7 - - + +
237A ILE 2.7 13.1 + - - +
238A ILE* 4.4 10.1 - - + -
239A ALA 3.2 24.9 + - - +
265A LEU* 1.3 72.9 - - - +
267A VAL* 1.3 60.1 + - - +
285A VAL* 3.8 5.6 - - - -
287A ILE* 3.9 21.1 - - + -
294A PHE* 3.3 15.7 - - + -
302A CYS* 4.7 2.2 - - - -
305A LEU* 4.1 16.8 - - + -
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Residues in contact with VAL 267 (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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239A ALA 3.4 13.9 - - - +
240A GLY* 4.5 2.9 - - - -
245A SER 5.6 0.7 - - - +
248A PRO* 3.5 33.2 - - + -
265A LEU* 3.9 16.2 - - + -
266A ALA* 1.3 78.2 - - - +
268A PRO* 1.4 81.4 - - + +
269A PHE 3.3 0.3 + - - -
271A GLN* 3.8 12.1 - - + +
272A ASN* 3.6 31.9 - - + +
275A ALA* 6.0 0.2 - - + -
284A SER* 4.2 5.6 - - - +
285A VAL 3.2 8.7 + - - +
286A PRO* 3.6 1.9 - - - +
287A ILE* 2.9 22.1 + - - +
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Residues in contact with PRO 268 (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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239A ALA 3.8 0.2 - - - +
240A GLY 3.5 26.0 - - - +
241A SER* 4.0 2.5 - - - +
267A VAL* 1.4 90.2 - - + +
269A PHE* 1.3 61.1 + - - +
271A GLN* 2.9 32.5 + - - +
272A ASN 3.2 6.8 + - - -
287A ILE* 3.3 10.8 - - + +
289A THR* 3.9 27.4 - - + +
292A GLY* 3.8 22.9 - - - +
294A PHE* 3.7 17.9 - - + +
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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