Contacts of the strand formed by residues 283 - 289 (chain A) in PDB entry 1RS0
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 ARG 283 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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243A SER* 2.8 30.7 + - - +
244A MET 2.9 10.3 + - - +
245A ASN* 2.8 45.7 + - - +
246A ILE 2.9 24.3 + - - -
281A LYS 5.6 0.4 - - - +
282A PRO* 1.3 74.1 - - - +
284A TYR* 1.3 61.0 + - - +
299A VAL* 3.2 28.6 - - + +
300A SER* 5.4 0.7 - - - +
304A SER* 3.7 15.0 - - - +
305A SER* 4.3 9.0 - - - +
355A THR* 4.3 3.8 + - - +
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Residues in contact with TYR 284 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246A ILE* 3.3 41.1 - - + +
248A LEU* 4.1 15.9 - - + -
271A LEU* 5.6 2.1 - - + +
272A ILE* 3.6 44.8 + - + +
275A VAL* 3.7 19.9 - - - +
282A PRO* 3.5 30.2 - - + +
283A ARG* 1.3 73.7 - - - +
285A GLY* 1.3 60.1 + - - +
297A VAL* 3.1 20.4 - - + +
299A VAL* 3.6 10.5 + - - -
304A SER* 2.9 29.7 + - - +
305A SER* 5.2 1.1 - - - -
307A ALA* 5.1 9.4 - - + -
310A VAL* 4.0 27.6 - - + -
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Residues in contact with GLY 285 (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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246A ILE 3.0 10.2 + - - -
247A TYR* 4.4 5.6 - - - -
248A LEU* 2.7 35.7 + - - +
284A TYR* 1.3 75.3 - - - +
286A LEU* 1.3 58.2 + - - -
287A VAL* 4.2 3.6 - - - -
297A VAL 3.3 9.9 - - - -
299A VAL* 4.2 3.3 - - - +
340A MET* 4.1 17.7 - - - -
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Residues in contact with LEU 286 (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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248A LEU* 3.7 27.1 - - + +
250A LEU* 5.7 2.0 - - + -
268A LEU* 4.9 3.6 - - + -
285A GLY* 1.3 74.2 - - - +
287A VAL* 1.3 69.6 + - - +
288A THR* 5.6 1.3 - - + -
295A ILE* 3.7 0.3 - - - -
296A TRP* 2.7 39.7 + - + -
297A VAL* 3.0 27.2 + - + +
310A VAL* 4.4 12.6 - - + +
313A GLN* 4.5 4.7 - - + -
314A LEU* 3.8 42.4 - - + +
317A ILE* 3.7 29.6 - - + -
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Residues in contact with VAL 287 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247A TYR* 6.3 0.4 - - + -
248A LEU 2.7 15.6 + - - +
249A VAL* 3.3 22.1 - - + -
250A LEU* 2.7 33.1 + - - +
285A GLY 4.8 1.1 - - - -
286A LEU* 1.3 82.9 - - - +
288A THR* 1.3 72.6 + - - +
289A TYR* 5.1 0.7 - - + -
293A PRO* 3.9 11.9 - - + -
294A LYS 3.3 12.3 - - - +
295A ILE* 3.8 19.1 - - + -
296A TRP* 4.3 0.2 - - - -
333A ALA* 4.9 2.7 - - - +
336A ALA* 4.7 6.3 - - + -
337A VAL* 5.1 3.8 - - + -
340A MET* 3.7 27.1 - - + -
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Residues in contact with THR 288 (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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250A LEU* 3.1 17.7 - - + +
252A GLY 5.4 0.9 - - - -
261A PHE* 4.4 15.3 - - + -
286A LEU* 5.6 1.6 - - + -
287A VAL* 1.3 79.5 - - - +
289A TYR* 1.3 65.6 + - - +
293A PRO* 3.3 1.4 - - - +
294A LYS* 2.8 28.6 + - - +
296A TRP* 2.9 32.8 + - + +
317A ILE* 4.2 24.9 - - + -
322A HIS* 2.7 29.4 + - - +
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Residues in contact with TYR 289 (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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249A VAL* 3.8 21.5 - - + -
250A LEU 3.0 15.8 + - - -
251A ASP* 3.5 29.3 - - + +
252A GLY 2.8 29.0 + - - +
287A VAL* 5.1 0.2 - - + -
288A THR* 1.3 78.3 - - - +
290A ALA* 1.3 69.1 + - - +
292A TYR 3.5 7.6 - - - +
293A PRO* 3.9 8.5 - - + -
322A HIS* 3.3 11.4 + - - -
328A THR* 4.1 11.4 - - + -
329A ASN 3.6 15.7 - - - +
330A THR* 3.3 43.4 + - - +
333A ALA* 3.5 17.0 - - + -
361A LEU* 3.6 8.0 - - + +
363A THR* 3.3 25.3 + - - -
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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