Contacts of the strand formed by residues 311 - 317 (chain F) in PDB entry 4P0S
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 THR 311 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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393E VAL* 4.6 14.8 - - + +
292F THR* 3.9 10.7 - - - +
293F TRP* 3.9 28.2 - - + -
309F GLU* 2.5 18.4 + - - +
310F PRO* 1.3 86.5 + - - +
312F VAL* 1.3 62.9 - - - +
357F LYS* 3.1 21.3 + - - +
358F ALA* 3.6 19.6 - - + +
439F PHE* 4.0 20.9 - - + -
443F VAL* 4.7 3.9 - - + +
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Residues in contact with VAL 312 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287F VAL* 4.2 1.3 - - + -
290F SER* 4.0 22.2 - - - -
291F VAL 3.5 7.9 - - - +
292F THR* 3.7 20.9 - - + -
293F TRP* 4.5 1.3 - - - -
311F THR* 1.3 76.9 - - - +
313F LEU* 1.3 61.1 + - - +
314F VAL* 4.0 7.4 - - + -
350F ILE* 5.3 1.6 - - + -
354F THR* 3.5 30.7 - - + +
357F LYS* 3.5 26.7 - - + +
358F ALA 3.2 11.9 + - - +
359F LEU* 3.1 24.5 - - + +
360F SER* 3.5 0.9 + - - -
439F PHE* 5.8 0.2 - - - -
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Residues in contact with LEU 313 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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290F SER* 3.5 0.9 - - - -
291F VAL* 2.7 56.4 + - + +
293F TRP* 4.1 12.2 - - + -
312F VAL* 1.3 73.0 - - - +
314F VAL* 1.3 73.0 + - - +
315F LEU* 4.3 3.8 - - + +
360F SER* 3.2 23.3 - - - +
362F VAL* 4.2 15.3 - - + -
435F PHE* 3.9 12.6 - - + -
436F THR* 5.9 4.7 - - + +
439F PHE* 3.4 46.0 - - + -
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Residues in contact with VAL 314 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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287F VAL* 4.2 14.4 - - + -
288F PRO 4.8 1.6 - - - +
289F CYS* 3.8 6.3 - - + +
290F SER* 3.6 22.7 - - - -
312F VAL* 4.0 7.4 - - + -
313F LEU* 1.3 74.1 - - - +
315F LEU* 1.3 68.4 + - - +
346F PHE* 4.7 8.7 - - + -
350F ILE* 4.2 21.8 - - + -
359F LEU* 3.4 23.6 - - + +
360F SER 2.9 14.7 + - - +
361F LEU* 2.7 42.7 - - + +
362F VAL 3.4 2.4 + - - -
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Residues in contact with LEU 315 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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260F LEU* 3.7 16.6 - - + -
263F MET* 3.7 36.3 - - + -
269F LEU* 5.5 0.7 - - + -
289F CYS* 3.0 34.8 + - + +
291F VAL* 5.8 0.4 - - - +
313F LEU* 4.3 5.3 + - + +
314F VAL* 1.3 76.3 - - - +
316F LEU* 1.3 83.3 + - - +
317F ARG 3.9 2.4 + - - +
346F PHE* 5.9 0.2 - - - -
362F VAL* 3.9 12.3 - - + +
364F VAL* 3.7 17.9 - - + -
429F TRP* 4.2 1.6 - - + -
432F LEU* 3.5 40.2 - - + -
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Residues in contact with LEU 316 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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289F CYS* 6.0 3.1 - - - -
314F VAL* 3.9 0.6 + - + -
315F LEU* 1.3 86.3 - - - +
317F ARG* 1.3 74.4 + - + +
320F ALA* 4.3 12.3 - - + -
321F PHE* 3.9 23.6 - - + +
324F MET* 3.7 27.4 - - + -
343F LEU* 6.3 0.7 - - + -
346F PHE* 4.3 24.0 - - + -
361F LEU* 3.9 31.9 - - + -
362F VAL 2.9 18.0 + - - +
363F ILE* 3.4 14.4 - - + +
364F VAL 3.5 3.6 + - - -
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Residues in contact with ARG 317 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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263F MET* 3.4 38.2 - - - +
264F GLU* 2.9 38.6 + - - -
289F CYS* 5.9 3.2 - - - -
315F LEU* 3.9 5.8 + - + +
316F LEU* 1.3 81.9 - - + +
318F ALA* 1.3 69.9 + - + +
319F GLU* 3.6 33.9 - - + +
320F ALA* 3.2 18.3 + - + +
321F PHE* 3.5 9.0 + - - +
364F VAL* 4.1 11.5 + - + +
429F TRP* 4.4 8.6 - - - -
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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