Contacts of the strand formed by residues 315 - 320 (chain A) in PDB entry 4CY1
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 315 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35A TYR* 3.8 1.1 + - - -
53A PHE* 4.0 19.0 - - + -
74A ALA 4.4 6.1 - - - +
75A TYR* 3.7 31.4 - - + -
309A CYS* 3.6 3.3 - - - +
310A HIS* 2.9 39.8 + - + +
313A GLU* 2.9 25.8 + - + -
314A ASN* 1.3 79.5 - - - +
316A ILE* 1.3 69.2 + - - +
329A LEU* 4.4 10.1 - - + -
330A TRP 3.3 11.4 - - - +
331A LYS* 4.0 30.7 - - + -
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Residues in contact with ILE 316 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A TYR* 3.5 41.3 - - + +
267A SER* 5.6 0.2 - - - +
275A VAL* 4.0 30.3 - - + -
283A VAL* 4.7 6.7 - - + -
285A ILE* 3.8 19.7 - - + -
297A LEU* 4.6 4.5 - - + -
307A THR* 4.6 5.2 - - + -
308A ALA 3.3 6.5 - - - +
309A CYS* 4.3 14.1 - - - -
315A ILE* 1.3 79.1 - - - +
317A ALA* 1.3 75.3 + - - +
318A SER* 4.6 0.7 - - - +
329A LEU* 3.4 2.9 - - - -
330A TRP* 2.8 50.7 + - + -
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Residues in contact with ALA 317 (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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51A VAL* 4.1 9.9 - - + -
53A PHE* 3.6 26.3 - - + -
60A LEU* 3.7 24.9 - - + -
307A THR* 3.1 4.0 - - - -
308A ALA* 2.8 34.2 + - + +
316A ILE* 1.3 75.7 - - - +
318A SER* 1.3 60.2 + - - +
327A ILE* 4.9 0.9 - - + -
328A LYS 3.2 5.8 - - - +
329A LEU* 3.8 8.3 - - + -
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Residues in contact with SER 318 (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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51A VAL* 4.5 1.1 - - - -
283A VAL* 3.8 20.4 - - - -
300A HIS* 2.7 26.4 + - - -
304A VAL* 4.0 3.1 - - - -
306A SER 3.2 9.6 - - - -
307A THR* 4.1 2.7 - - - -
316A ILE* 4.9 0.7 - - - -
317A ALA* 1.3 75.2 - - - +
319A ALA* 1.3 60.5 - - - +
327A ILE* 3.2 7.2 - - - +
328A LYS* 2.8 31.9 + - - +
330A TRP* 2.8 28.0 + - - -
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Residues in contact with ALA 319 (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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48A VAL* 3.5 31.4 - - + -
51A VAL* 3.7 17.9 - - + -
300A HIS* 4.1 2.9 - - - -
304A VAL* 3.4 5.9 - - - +
305A ILE* 3.0 24.5 + - + -
306A SER* 2.9 19.2 + - - +
318A SER* 1.3 75.5 - - - +
320A ALA* 1.3 61.8 + - - +
326A THR 3.6 5.8 - - - -
327A ILE* 3.9 5.4 - - + -
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Residues in contact with ALA 320 (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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48A VAL* 3.2 28.1 + - - +
300A HIS* 3.5 11.2 - - + +
302A ASP 3.8 9.4 - - - +
303A VAL 3.2 13.5 - - - +
304A VAL* 4.5 0.2 - - - -
305A ILE 4.4 0.2 - - - +
319A ALA* 1.3 76.4 - - - +
321A LEU* 1.3 66.7 + - - +
324A ASP* 3.4 35.0 - - + +
325A LYS* 3.8 6.3 + - - -
326A THR 3.4 6.4 + - - +
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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