Contacts of the strand formed by residues 314 - 318 (chain F) in PDB entry 6Q2J
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 TYR 314 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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266F ASP* 4.5 0.2 + - - -
300F ASP* 3.8 11.4 + - - -
302F ASP* 5.1 1.9 - - - +
303F VAL 5.3 0.7 + - - -
305F PRO* 3.3 44.7 + - + +
310F LEU* 3.0 45.4 + - + +
311F VAL* 4.1 6.6 - - - +
313F ARG* 1.3 81.7 - - - +
315F THR* 1.3 64.3 + - - +
316F SER 3.7 1.6 + - - -
333F HIS* 4.2 23.8 - - + +
350F THR* 4.7 7.9 + - + +
352F HIS* 3.3 34.2 + + - -
354F TYR* 5.1 6.5 - - - +
376F VAL* 6.4 1.6 - - + -
377F ASN 3.3 3.8 - - - -
378F ASP* 3.2 38.1 + - + -
379F SER 4.6 0.2 - - - -
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Residues in contact with THR 315 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311F VAL 4.4 11.7 - - - +
312F ARG* 4.5 6.7 - - - +
313F ARG 3.7 2.0 - - - +
314F TYR* 1.3 79.5 - - - +
316F SER* 1.3 59.0 + - - +
317F THR* 4.0 9.9 + - - -
354F TYR* 5.5 0.9 - - - -
375F LEU 3.5 3.1 - - - +
376F VAL* 4.8 0.7 - - - -
377F ASN* 2.9 52.3 + - - +
703F NAG 3.7 27.9 + - + +
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Residues in contact with SER 316 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314F TYR 3.7 3.6 + - - -
315F THR* 1.3 70.8 - - - +
317F THR* 1.3 61.4 + - - +
318F LEU 4.1 1.2 + - - -
331F VAL* 4.4 15.1 + - - +
333F HIS* 4.1 14.2 - - - +
354F TYR* 3.5 33.4 - - - -
374F VAL* 4.6 7.9 - - - -
375F LEU 3.2 7.9 - - - -
376F VAL* 4.8 0.4 - - - +
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Residues in contact with THR 317 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315F THR* 4.0 12.0 + - - -
316F SER* 1.3 73.2 + - - +
318F LEU* 1.3 73.2 + - - +
319F LEU* 3.4 13.8 + - + -
320F PRO* 5.9 1.3 - - + -
374F VAL* 3.7 3.0 - - - -
375F LEU* 2.9 52.6 + - + +
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Residues in contact with LEU 318 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316F SER 4.1 2.4 + - - -
317F THR* 1.3 79.0 - - - +
319F LEU* 1.3 75.0 + - - +
320F PRO* 3.7 2.6 - - - +
325F ALA* 5.4 2.0 - - + -
326F GLN* 3.8 29.2 + - + +
329F PHE* 4.0 26.5 - - + +
330F ARG* 5.0 0.9 - - - -
331F VAL* 3.7 35.7 - - + +
356F LEU* 5.3 0.9 - - + -
372F LEU* 4.7 24.2 - - + -
373F ALA 3.9 11.9 - - - +
374F VAL* 4.0 7.9 - - + +
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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
------------------------------------------------------------
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