Contacts of the strand formed by residues 310 - 315 (chain D) 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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235D TYR* 3.8 15.0 - - + -
237D LEU* 3.9 33.4 - - + -
299D TYR* 4.2 12.3 - + + -
304D HIS* 3.7 22.7 - + - +
309D CYS* 1.3 74.2 - - - +
311D ILE* 1.3 74.1 + - - +
312D CYS* 4.1 15.3 - - + -
340D PHE* 3.7 48.7 - + - -
348D LEU* 3.6 24.7 - - + -
352D PRO 3.1 9.9 + - - +
353D LYS* 3.5 6.9 - - + -
354D VAL* 2.9 25.3 + - - +
355D PHE* 4.3 9.9 - + - -
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Residues in contact with ILE 311 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235D TYR 3.0 10.1 + - - +
236D CYS* 3.3 20.7 - - - -
237D LEU* 2.8 25.2 + - - +
274D PHE* 3.4 35.7 - - + -
279D PHE* 3.5 32.8 - - + -
309D CYS* 4.1 5.6 - - - -
310D PHE* 1.3 85.5 - - - +
312D CYS* 1.3 64.1 + - - +
313D CYS* 4.1 4.7 - - - -
354D VAL* 3.2 15.9 - - + +
356D PHE* 4.1 25.1 - - + -
476D PHE* 4.2 9.2 - - + -
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Residues in contact with CYS 312 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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237D LEU* 3.6 17.5 - - + -
239D ILE* 4.3 4.5 - - - -
296D LEU* 4.2 19.1 - - - -
310D PHE* 4.1 13.2 - - + -
311D ILE* 1.3 75.6 - - - +
313D CYS* 1.3 64.3 + - - +
314D ILE* 4.0 21.8 + - - +
354D VAL 2.8 8.9 + - - -
355D PHE* 3.2 36.4 - - + +
356D PHE 2.9 24.3 + - - +
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Residues in contact with CYS 313 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236D CYS* 4.1 10.8 - - - -
237D LEU 2.7 18.7 + - - +
238D ILE* 3.4 7.8 - - + -
239D ILE* 2.8 33.0 + - - +
270D LEU* 3.9 37.2 - - + -
274D PHE* 4.9 0.9 - - - -
311D ILE* 4.1 10.3 - - - -
312D CYS* 1.3 73.9 - - - +
314D ILE* 1.3 60.5 - - - +
315D LEU* 4.1 4.9 - - + -
356D PHE* 3.4 30.7 - - + +
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Residues in contact with ILE 314 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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239D ILE* 3.6 26.7 - - + +
292D ILE* 5.3 1.6 - - + -
296D LEU* 5.6 0.9 - - + -
312D CYS* 4.0 20.4 - - - +
313D CYS* 1.3 77.0 - - - +
315D LEU* 1.3 65.0 + - - +
316D SER* 4.5 8.5 - - - -
323D ILE* 4.0 34.8 - - + -
336D LEU* 3.6 33.0 - - + -
355D PHE* 5.1 2.2 - - + -
356D PHE 2.9 8.4 + - - +
357D ILE* 3.9 24.7 - - + -
358D GLN 2.9 28.5 + - - +
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Residues in contact with LEU 315 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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238D ILE* 4.0 23.3 - - + -
239D ILE 2.8 15.0 + - - +
240D ASN* 3.6 17.7 - - - +
241D ASN* 2.9 24.8 + - - +
260D ARG* 3.4 19.2 + - - +
263D THR* 3.8 7.4 - - - +
266D ASP* 4.1 17.7 - - + +
267D ALA 4.1 8.1 - - - +
270D LEU* 4.0 11.4 - - + -
313D CYS* 4.6 1.8 - - + -
314D ILE* 1.3 84.9 - - - +
316D SER* 1.3 63.4 + - - +
358D GLN* 3.6 10.3 - - + -
422D ILE* 3.9 32.5 - - + -
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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