Contacts of the strand formed by residues 259 - 265 (chain A) in PDB entry 4Y05
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 ILE 259 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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257A HIS* 3.5 4.3 - - - +
258A ARG* 1.3 82.4 - - + +
260A CYS* 1.3 61.0 + - - +
261A VAL* 4.0 9.9 - - + -
527A ILE* 3.9 25.6 - - + +
530A LEU* 3.5 38.1 - - + -
531A GLY* 3.8 24.9 - - - +
559A THR* 3.5 12.1 - - + -
585A VAL* 4.4 2.2 - - + +
586A LYS* 3.0 58.2 + - + +
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Residues in contact with CYS 260 (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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257A HIS* 3.9 17.7 - - + +
259A ILE* 1.3 74.2 - - - +
261A VAL* 1.3 62.1 + - - +
262A CYS* 3.6 25.1 - - - -
312A ASP* 3.4 7.6 - - - -
313A PHE* 3.9 21.8 - - - -
327A PHE 4.0 11.9 - - - -
328A THR 5.5 1.1 - - - +
332A LEU* 6.4 1.6 - - + -
559A THR* 2.9 14.4 + - - +
560A CYS* 3.3 13.0 - - + -
561A MET 2.8 27.2 + - - +
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Residues in contact with VAL 261 (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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259A ILE* 4.0 5.2 - - + -
260A CYS* 1.3 77.5 - - - +
262A CYS* 1.3 64.4 + - - +
311A PHE* 3.5 14.6 - - + +
312A ASP* 2.8 44.8 + - - +
561A MET* 3.5 14.6 - - + +
582A ALA* 3.6 37.7 - - + +
585A VAL* 3.6 27.8 - - + -
586A LYS* 3.6 24.2 - - + +
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Residues in contact with CYS 262 (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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260A CYS* 3.6 25.6 - - - -
261A VAL* 1.3 81.3 - - - +
263A VAL* 1.3 61.0 + - - +
311A PHE* 4.6 1.3 - - - -
313A PHE* 3.2 27.6 - - - +
315A PHE* 3.9 13.7 - - + -
328A THR* 3.6 23.3 - - + -
560A CYS* 4.3 0.9 - - - -
561A MET 2.8 13.6 + - - +
562A ILE* 4.3 8.5 - - + -
563A ALA* 2.8 33.6 + - - +
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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
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262A CYS* 1.3 78.5 - - - +
264A ARG* 1.3 56.6 + - - +
283A ILE* 5.2 0.7 - - + -
289A LEU* 3.6 25.4 - - + -
311A PHE* 3.3 49.4 - - + -
313A PHE 3.1 2.4 + - - -
314A ALA* 3.7 19.5 - - + -
315A PHE* 2.7 38.3 + - - +
562A ILE* 5.0 0.4 - - - -
563A ALA* 3.1 16.8 - - + +
565A ILE* 5.3 2.2 - - + -
579A LEU* 3.7 13.5 - - + -
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Residues in contact with ARG 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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263A VAL* 1.3 75.3 - - - +
265A LYS* 1.3 67.2 + - - +
266A ARG* 3.8 1.6 + - - +
315A PHE* 3.5 18.6 - - + +
316A ASP 5.1 0.8 + - - +
319A ALA 3.0 26.1 + - - -
320A SER* 3.6 7.9 - - - +
321A ASN* 2.8 30.5 + - - +
324A VAL* 3.6 23.2 - - - +
352A SER 4.8 0.7 - - - +
353A GLY* 6.2 0.7 - - - -
356A HIS* 3.8 5.2 + - - -
357A THR* 2.9 35.6 + - - +
562A ILE* 4.0 16.4 - - + -
563A ALA 2.8 9.2 + - - +
564A THR* 3.4 9.1 - - + -
565A ILE* 2.9 30.5 + - - +
702A ADP 3.5 26.4 + - - -
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Residues in contact with LYS 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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240A ARG* 4.4 1.2 - - - +
263A VAL* 4.2 0.6 - - - +
264A ARG* 1.3 78.1 + - - +
266A ARG* 1.3 68.5 + - - +
267A PRO* 5.5 0.7 - - - -
279A ASP* 2.7 36.9 + - - -
281A ILE* 2.9 34.4 + - + +
282A SER* 5.1 0.6 - - - +
283A ILE* 4.1 14.8 - - + +
315A PHE 2.9 13.9 + - - +
316A ASP* 3.5 5.0 - - - +
317A GLU* 3.1 58.8 + - - +
565A ILE* 3.8 15.5 - - + +
567A PRO* 3.6 17.9 - - + -
702A ADP 4.8 1.6 + - - -
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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