Contacts of the strand formed by residues 310 - 315 (chain A) in PDB entry 4PS1
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 PHE 310 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235A TYR* 3.8 13.0 - - + -
237A LEU* 3.8 39.7 - - + -
299A TYR* 4.1 12.6 - + + -
304A HIS* 3.8 19.5 - + - +
309A CYS* 1.3 75.0 - - - +
311A ILE* 1.3 70.8 + - - +
312A CYS* 4.1 16.4 - - + -
340A PHE* 3.7 47.1 - + - -
348A LEU* 3.5 24.9 - - + -
352A PRO 3.1 9.2 + - - +
353A LYS* 3.5 7.2 - - + -
354A VAL* 2.8 25.1 + - - +
355A PHE* 4.3 10.1 - + - -
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Residues in contact with ILE 311 (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 TYR 3.0 11.1 + - - +
236A CYS* 3.3 20.2 - - - -
237A LEU* 2.9 26.7 + - - +
274A PHE* 3.5 33.7 - - + -
279A PHE* 3.5 32.3 - - + -
309A CYS* 4.1 3.6 - - - -
310A PHE* 1.3 83.6 - - - +
312A CYS* 1.3 64.2 + - - +
313A CYS* 4.0 13.7 - - - -
354A VAL* 3.2 18.8 - - + +
356A PHE* 4.1 15.7 - - + -
476A PHE* 4.2 10.3 - - + -
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Residues in contact with CYS 312 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237A LEU* 3.7 14.8 - - + -
239A ILE* 4.7 5.2 - - - -
296A LEU* 4.1 21.3 - - - -
310A PHE* 4.1 10.3 - - + -
311A ILE* 1.3 75.8 - - - +
313A CYS* 1.3 63.6 + - - +
314A ILE* 4.1 18.5 - - - +
354A VAL 2.8 8.9 + - - -
355A PHE* 3.2 41.4 - - + +
356A PHE 3.0 23.4 + - - +
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Residues in contact with CYS 313 (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 CYS* 4.1 10.8 - - - -
237A LEU 2.8 16.8 + - - +
238A ILE* 3.4 6.9 - - + +
239A ILE* 2.8 32.6 + - - +
270A LEU* 3.8 42.6 - - + -
274A PHE* 4.8 0.9 - - - -
311A ILE* 4.0 17.7 - - - -
312A CYS* 1.3 75.5 - - - +
314A ILE* 1.3 58.4 + - - +
315A LEU* 4.8 3.4 - - + -
356A PHE* 3.5 19.7 - - + +
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Residues in contact with ILE 314 (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 ILE* 3.7 22.0 - - + +
292A ILE* 5.4 4.5 - - + -
296A LEU* 5.7 1.6 - - + -
312A CYS* 4.1 20.2 - - - +
313A CYS* 1.3 77.7 - - - +
315A LEU* 1.3 61.3 + - - +
316A SER* 4.5 8.3 - - - +
323A ILE* 4.1 35.7 - - + -
336A LEU* 3.5 34.1 - - + -
355A PHE* 4.8 2.9 - - + -
356A PHE 2.9 8.1 + - - +
357A ILE* 3.8 23.1 - - + -
358A GLN* 2.8 33.0 + - - +
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Residues in contact with LEU 315 (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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238A ILE* 3.9 24.0 - - + -
239A ILE 2.9 15.2 + - - +
240A ASN* 3.6 19.3 - - - +
241A ASN* 2.9 29.6 + - - +
260A ARG* 3.4 9.3 + - - +
263A THR* 3.7 17.3 - - - +
266A ASP* 3.9 18.2 - - + +
267A ALA 4.1 5.8 - - - +
270A LEU* 4.1 11.0 - - + -
313A CYS* 4.8 0.9 - - + -
314A ILE* 1.3 82.7 - - - +
316A SER* 1.3 63.1 + - - +
356A PHE 5.6 0.4 - - - +
358A GLN* 3.6 9.0 - - + -
422A ILE* 3.8 33.4 - - + -
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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