Contacts of the strand formed by residues 408 - 417 (chain A) in PDB entry 3NVQ
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 408 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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304A GLN* 3.3 23.9 - - - +
324A VAL* 3.6 23.1 - - + +
326A SER* 5.1 0.2 - - - -
332A SER* 2.9 31.4 + - - +
334A VAL* 5.2 2.7 - - + -
402A PHE* 4.0 22.6 - + - -
404A SER* 3.6 22.6 + - - -
406A TYR* 3.8 9.3 - - + +
407A HIS* 1.3 75.4 + - - +
409A GLN* 1.3 59.7 + - - +
410A LYS 5.0 0.2 - - - +
429A LEU* 3.7 34.6 - - + +
430A THR 3.3 13.2 - - - +
431A THR* 3.8 17.0 - - + -
437A HIS* 2.7 35.9 + + - +
452A ASN* 3.6 10.9 + - - -
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Residues in contact with GLN 409 (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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4A NDG 4.4 12.3 + - - -
304A GLN* 3.8 24.9 + - - +
305A ASP* 3.3 15.9 - - - +
324A VAL* 5.2 2.0 - - - -
407A HIS* 4.2 13.6 + - + +
408A TYR* 1.3 79.0 - - - +
410A LYS* 1.3 70.5 + - + +
430A THR* 2.9 18.3 + - - +
431A THR 3.7 4.9 - - - +
432A ASP* 3.5 34.8 - - + +
464A ALA* 6.1 1.0 - - - +
465A ILE 5.0 6.9 + - - +
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Residues in contact with LYS 410 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305A ASP* 3.3 16.6 + - - +
324A VAL* 4.3 3.5 - - - +
408A TYR 4.0 0.2 - - - -
409A GLN* 1.3 89.3 - - + +
411A VAL* 1.3 61.7 + - - +
428A TYR 3.5 0.2 - - - +
429A LEU* 3.2 11.1 - - - +
430A THR* 3.2 39.1 + - + +
465A ILE 4.0 10.5 - - - +
466A GLN 3.5 31.8 + - - -
467A THR* 4.2 4.9 - - - +
468A MET* 3.6 33.0 - - + +
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Residues in contact with VAL 411 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305A ASP* 3.0 20.7 + - - +
306A VAL 4.8 0.3 - - - +
307A PHE* 3.5 23.3 - - + +
322A TYR* 3.9 25.8 - - + +
324A VAL* 3.3 28.3 - - + -
334A VAL* 5.1 2.5 - - + -
410A LYS* 1.3 73.5 - - - +
412A ALA* 1.3 73.2 + - - +
413A VAL* 4.5 10.3 - - + -
427A LEU* 4.7 11.0 - - + -
428A TYR 3.3 6.3 - - - +
429A LEU* 3.5 20.0 - - + -
468A MET* 3.6 4.2 - - - +
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Residues in contact with ALA 412 (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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307A PHE* 3.8 12.6 - - + -
411A VAL* 1.3 77.5 - - - +
413A VAL* 1.3 63.2 + - - +
427A LEU* 3.5 2.6 - - - -
428A TYR* 2.8 40.9 + - + -
468A MET* 3.9 17.3 - - + +
469A SER* 5.9 0.7 - - - -
470A LEU* 3.7 30.7 - - + +
477A LEU* 4.6 0.2 - - + -
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Residues in contact with VAL 413 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307A PHE* 3.3 32.0 - - + -
309A LEU* 4.0 25.9 - - + +
322A TYR* 3.6 47.8 - - + -
411A VAL* 4.5 3.8 - - + -
412A ALA* 1.3 79.5 - - - +
414A HIS* 1.3 63.9 + - - +
415A ARG 4.2 0.2 - - - -
425A HIS* 4.2 17.5 - - + -
426A VAL 3.5 11.0 - - - +
427A LEU* 4.4 11.4 - - + -
470A LEU* 3.3 10.2 - - - +
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Residues in contact with HIS 414 (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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413A VAL* 1.3 77.3 - - - +
415A ARG* 1.3 73.2 + - - +
416A MET* 3.6 17.9 + - + +
424A PHE 3.6 1.7 - - - +
426A VAL* 3.0 32.3 + - - +
428A TYR* 4.1 9.4 - - + -
470A LEU* 3.6 12.3 - - + +
472A ALA* 3.6 41.7 - - + +
475A ARG* 4.6 8.9 + - - +
490A LEU* 3.5 16.4 - - + +
510A TYR* 2.7 36.5 - + - +
522A TYR* 4.4 5.3 + - - -
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Residues in contact with ARG 415 (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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309A LEU* 3.5 31.4 - - + +
310A PRO 2.5 29.7 + - - -
311A ASP* 4.6 3.2 + - - +
312A PRO* 3.5 37.4 - - - +
320A ARG* 5.0 6.3 - - - +
413A VAL* 4.2 1.4 + - - +
414A HIS* 1.3 86.0 + - - +
416A MET* 1.3 63.0 + - - +
417A GLN* 4.3 9.5 + - - +
423A THR* 3.6 24.7 - - + -
424A PHE 3.5 4.9 - - - -
425A HIS* 3.3 34.7 + - + +
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Residues in contact with MET 416 (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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414A HIS* 3.7 20.9 - - + +
415A ARG* 1.3 78.0 - - - +
417A GLN* 1.3 87.3 + - - +
418A ALA* 3.9 1.6 - - - -
423A THR* 3.1 6.2 - - - +
424A PHE* 2.9 74.3 + - + +
426A VAL* 3.5 22.9 - - + -
509A PRO* 3.8 26.5 - - + +
510A TYR* 4.2 12.8 - - + -
521A ILE* 5.1 1.1 - - + -
522A TYR* 3.3 19.5 - - + +
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Residues in contact with GLN 417 (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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415A ARG* 4.3 10.2 + - - +
416A MET* 1.3 90.4 - - - +
418A ALA* 1.3 68.7 + - - +
421A GLY* 3.9 15.7 - - - +
422A GLU 2.9 4.3 - - - +
423A THR* 2.9 29.7 + - - +
521A ILE* 3.6 17.0 - - - +
522A TYR* 4.2 7.1 + - - -
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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