Contacts of the strand formed by residues 368 - 378 (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 ARG 368 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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322F ASP* 2.5 39.0 + - - +
324F TRP* 3.3 54.1 - - + +
366F GLU* 6.2 0.7 - - - -
367F ASN* 1.3 85.2 + - - +
369F THR* 1.3 69.9 + - - +
370F MET* 4.9 8.4 - - + +
396F SER* 3.5 3.6 - - - -
397F VAL* 2.9 45.4 + - + +
398F LEU* 6.1 0.2 - - - +
706F NAG 5.0 8.7 - - + -
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Residues in contact with THR 369 (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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368F ARG* 1.3 81.4 + - - +
370F MET* 1.3 68.8 + - - +
395F VAL 3.8 5.2 - - - -
396F SER* 3.2 18.1 + - - -
706F NAG 5.5 9.4 - - + +
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Residues in contact with MET 370 (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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322F ASP* 5.8 3.4 - - + +
324F TRP* 3.6 32.3 - - + -
325F ALA* 3.7 33.4 - - + +
329F PHE* 3.8 27.8 - - + -
368F ARG* 4.9 9.6 - - + +
369F THR* 1.3 86.5 + - - +
371F GLN* 1.3 61.2 + - - +
372F LEU* 3.9 18.4 - - + -
393F PHE 3.8 0.2 - - - +
394F ASN* 3.5 5.7 - - - +
395F VAL* 2.8 46.3 + - + +
397F VAL* 5.1 2.9 - - - -
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Residues in contact with GLN 371 (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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370F MET* 1.3 74.8 - - - +
372F LEU* 1.3 73.4 + - - +
373F ALA* 4.3 2.0 + - + +
392F HIS* 4.2 23.1 + - + +
393F PHE 3.4 5.6 - - - +
394F ASN* 4.1 16.3 + - - +
704F NAG 4.7 17.4 - - - -
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Residues in contact with LEU 372 (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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318F LEU* 4.7 19.5 - - + -
319F LEU 5.7 3.1 - - - +
321F GLY* 6.5 0.9 - - - -
325F ALA* 3.8 25.8 - - + -
329F PHE* 4.4 16.8 - - + -
356F LEU* 3.8 33.2 - - + -
370F MET* 3.9 23.1 - - + -
371F GLN* 1.3 82.5 - - - +
373F ALA* 1.3 60.2 + - - +
391F LEU 4.0 0.2 - - - +
392F HIS* 3.5 6.1 + - - +
393F PHE* 2.9 48.2 + - + +
395F VAL* 5.1 6.1 - - + -
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Residues in contact with ALA 373 (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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318F LEU* 3.9 3.0 - - - +
319F LEU* 3.1 53.9 + - + +
371F GLN* 4.3 2.4 + - + +
372F LEU* 1.3 76.0 - - - +
374F VAL* 1.3 62.5 + - - +
390F LEU* 4.2 7.9 - - + -
391F LEU 3.3 8.7 - - - +
392F HIS* 4.6 10.8 - - + +
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Residues in contact with VAL 374 (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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316F SER* 4.6 8.7 - - - -
317F THR 3.7 7.9 - - - +
318F LEU* 4.0 7.6 - - + -
331F VAL* 3.8 41.3 - - + -
354F TYR* 4.8 2.5 - - + -
356F LEU* 5.0 0.4 - - + -
373F ALA* 1.3 77.9 - - - +
375F LEU* 1.3 70.0 + - - +
376F VAL* 4.0 0.6 + - + -
390F LEU* 3.6 5.5 - - - +
391F LEU* 2.8 56.6 + - + +
393F PHE* 3.7 29.6 - - + -
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Residues in contact with LEU 375 (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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315F THR 3.5 1.8 - - - +
316F SER* 3.2 7.8 - - - -
317F THR* 2.9 52.3 + - + +
319F LEU* 4.5 19.1 - - + -
373F ALA 4.3 0.4 + - - -
374F VAL* 1.3 72.3 - - - +
376F VAL* 1.3 64.7 + - - +
377F ASN* 4.2 7.2 - - + +
388F VAL* 3.7 24.5 - - + -
389F LEU 3.4 15.5 - - - +
390F LEU* 4.1 15.7 - - + -
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Residues in contact with VAL 376 (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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270F PRO* 5.1 6.1 - - + -
298F VAL* 4.8 13.9 - - + -
314F TYR* 6.4 2.0 - - + -
315F THR 3.8 2.5 - - - +
352F HIS* 6.3 1.8 - - + -
354F TYR* 3.3 48.9 - - + +
374F VAL* 4.7 1.6 - - + +
375F LEU* 1.3 76.3 - - - +
377F ASN* 1.3 65.9 + - - +
378F ASP* 4.8 4.5 - - + +
387F GLY 4.0 0.9 - - - +
388F VAL* 3.4 7.3 - - - +
389F LEU* 2.9 49.1 + - + +
391F LEU* 4.2 22.9 - - + -
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Residues in contact with ASN 377 (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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313F ARG 3.1 8.5 - - - +
314F TYR* 3.3 4.0 - - - -
315F THR* 2.9 46.6 + - - +
375F LEU* 5.7 6.0 - - + +
376F VAL* 1.3 74.8 - - - +
378F ASP* 1.3 61.9 + - - +
379F SER* 3.5 7.8 + - - -
387F GLY 4.1 2.1 - - - +
388F VAL* 3.8 17.8 - - + +
703F NAG 1.5 64.5 + - - +
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Residues in contact with ASP 378 (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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266F ASP* 3.6 11.4 - - - +
270F PRO* 3.7 23.3 - - + +
300F ASP* 2.2 32.8 - - - +
305F PRO* 4.7 0.2 - - - +
314F TYR* 3.2 27.4 - - + -
352F HIS* 5.1 1.3 + - - -
376F VAL* 4.0 4.7 - - + -
377F ASN* 1.3 70.7 + - - +
379F SER* 1.3 60.3 + - - +
387F GLY* 3.3 25.4 + - - +
708F CA 2.4 18.7 - - - -
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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