Contacts of the strand formed by residues 277 - 284 (chain A) in PDB entry 1Y7V
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 277 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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228A TRP* 2.9 24.3 + - + +
229A ALA* 3.1 10.5 - - + +
230A VAL* 2.9 27.4 + - - +
268A LEU* 5.9 0.2 - - - -
275A ASN 4.2 9.4 + - - +
276A VAL* 1.3 77.3 - - - +
278A LEU* 1.3 61.5 + - - +
279A LEU* 4.8 1.3 - - + -
306A HIS* 3.1 49.7 + - - +
504A SO4 2.9 43.8 + - - +
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Residues in contact with LEU 278 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230A VAL* 3.5 20.9 - - + +
232A ALA* 4.1 7.2 - - + +
260A ILE* 3.6 33.2 - - + -
264A LEU* 3.7 34.3 - - + -
265A GLY* 4.8 2.0 - - - +
268A LEU* 4.5 14.4 - - + -
276A VAL 4.0 1.1 + - - +
277A ARG* 1.3 77.2 - - - +
279A LEU* 1.3 74.9 + - - +
304A TYR* 3.6 24.7 + - + +
305A VAL* 3.8 4.9 - - + +
306A HIS* 2.8 34.0 + - - +
307A GLY 3.4 3.1 + - - -
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Residues in contact with LEU 279 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175A LEU* 4.2 18.2 - - + -
228A TRP* 4.4 9.2 - - + -
229A ALA* 4.4 13.7 - - + -
230A VAL 2.9 15.6 + - - +
231A THR* 3.5 3.9 - - + -
232A ALA* 3.1 26.2 + - - +
278A LEU* 1.3 84.9 - - - +
280A MET* 1.3 61.9 + - - +
306A HIS* 4.2 13.9 - - - +
307A GLY* 3.0 24.0 - - - +
309A ALA* 3.8 29.8 - - + +
335A MET* 4.3 8.1 - - + -
337A PHE* 4.2 23.3 - - + -
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Residues in contact with MET 280 (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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232A ALA* 4.4 5.8 - - - -
256A GLN* 3.7 12.6 - - - +
260A ILE* 4.4 6.7 - - + -
279A LEU* 1.3 74.4 - - - +
281A LEU* 1.3 82.2 + - + +
282A ASP* 2.9 5.3 + - - -
291A TRP* 3.6 31.9 - - + +
292A ALA* 4.1 5.2 - - - +
295A VAL* 3.7 29.6 - - + -
296A LEU* 4.2 14.4 - - - -
305A VAL* 3.5 27.9 - - + +
307A GLY 2.8 13.3 + - - +
308A ILE* 3.9 20.6 - - + -
309A ALA* 2.8 26.9 + - - +
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Residues in contact with LEU 281 (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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232A ALA* 6.0 0.2 - - - -
233A GLU 3.6 0.9 - - - +
236A PRO* 2.9 26.7 - - - +
256A GLN* 3.1 17.9 + - - +
280A MET* 1.3 80.2 - - + +
282A ASP* 1.3 73.9 + - - +
283A ASP* 3.1 32.9 + - + +
284A GLN 4.3 5.4 - - - +
287A LEU* 3.9 8.5 - - + -
288A LEU* 3.5 41.1 - - + -
291A TRP* 3.7 33.7 - - + -
308A ILE* 3.9 9.9 - - + -
309A ALA 3.4 9.4 - - - +
310A VAL* 4.0 2.2 - - + -
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Residues in contact with ASP 282 (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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120A ARG* 2.9 17.5 + - - -
231A THR* 2.7 40.7 + - + +
232A ALA 5.2 0.2 - - - +
233A GLU 3.3 14.5 - - - +
234A ASN* 3.4 3.5 - - - -
235A GLU 2.8 20.3 + - - -
280A MET 2.9 4.9 + - - +
281A LEU* 1.3 72.8 - - - +
283A ASP* 1.3 54.3 + - - +
309A ALA* 2.6 24.4 + - + -
311A HIS* 2.6 26.1 + - - -
339A SER* 2.5 33.4 + - - -
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Residues in contact with ASP 283 (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 GLU* 3.1 26.4 - - - +
236A PRO* 3.3 0.7 - - + +
237A SER* 2.8 44.3 + - - -
281A LEU* 3.1 18.9 - - + +
282A ASP* 1.3 78.9 - - - +
284A GLN* 1.3 88.6 + - - +
287A LEU* 3.4 22.3 - - + +
309A ALA 3.6 0.4 + - - -
310A VAL* 3.5 5.5 - - - -
311A HIS* 2.9 24.7 + - - -
313A TYR* 4.8 0.2 + - - -
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Residues in contact with GLN 284 (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 GLU* 4.6 1.0 + - - -
237A SER* 4.7 7.1 + - - -
281A LEU* 4.3 2.8 - - - +
283A ASP* 1.3 93.4 + - - +
285A ARG* 1.3 63.7 + - - +
286A LEU* 3.1 20.0 + - - +
287A LEU* 3.2 29.4 + - + +
311A HIS* 3.5 13.3 - - - +
312A TRP* 3.2 31.1 - - + -
313A TYR* 3.8 14.6 + - + -
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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