Contacts of the strand formed by residues 371 - 384 (chain A) in PDB entry 3SV1
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 ILE 371 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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366A ASP* 4.2 14.6 - - + +
367A LEU* 4.6 11.7 - - + -
370A GLY* 1.3 80.5 - - - +
372A ILE* 1.3 72.9 + - - +
373A PHE* 3.5 32.3 - - + -
433A PHE* 3.3 1.2 - - - -
434A ILE* 2.8 47.6 + - + +
516A SER* 3.9 19.7 - - - +
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Residues in contact with ILE 372 (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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371A ILE* 1.3 85.0 - - - +
373A PHE* 1.3 68.8 + - - +
431A ASP* 3.5 35.4 - - + +
432A LEU 2.8 12.3 - - - +
433A PHE* 4.1 20.6 - - + +
447A GLN* 5.9 4.5 - - - +
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Residues in contact with PHE 373 (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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371A ILE* 3.5 31.6 - - + -
372A ILE* 1.3 78.1 - - - +
374A ALA* 1.3 62.3 + - - +
375A ALA 3.6 0.3 + - - -
431A ASP* 3.3 4.2 - - - -
432A LEU* 2.7 43.2 + - + +
434A ILE* 4.0 10.5 - - + -
509A ASP* 4.2 28.3 - - + -
512A LEU* 4.2 20.0 - - + -
513A ILE* 3.6 35.0 - - + -
516A SER* 3.6 15.0 - - - -
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Residues in contact with ALA 374 (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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373A PHE* 1.3 74.0 - - - +
375A ALA* 1.3 61.0 + - - +
430A VAL 3.5 7.6 - - - +
431A ASP* 4.1 9.2 - - - +
507A SER* 3.0 18.0 + - - -
509A ASP* 4.9 4.6 + - - +
513A ILE* 4.5 1.4 - - - +
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Residues in contact with ALA 375 (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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373A PHE 3.6 0.4 + - - -
374A ALA* 1.3 76.4 - - - +
376A ASN* 1.3 73.6 + - - +
429A GLU* 3.7 2.3 - - - +
430A VAL* 2.8 36.2 + - + +
432A LEU* 3.9 28.3 - - + -
505A PHE* 4.2 9.6 - - + -
506A GLU 3.6 9.9 - - - +
507A SER* 4.0 11.0 - - - -
513A ILE* 4.5 0.7 - - + -
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Residues in contact with ASN 376 (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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375A ALA* 1.3 86.6 + - - +
377A TYR* 1.3 64.1 + - - +
378A LEU* 3.4 4.8 - - + +
427A LEU* 3.5 22.7 - - - +
428A THR 3.3 5.9 + - - -
429A GLU* 3.2 29.3 - - - +
505A PHE* 2.9 5.8 - - - -
506A GLU* 2.6 60.6 + - - +
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Residues in contact with TYR 377 (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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376A ASN* 1.3 71.2 - - - +
378A LEU* 1.3 68.2 + - - +
379A GLY* 3.1 35.3 - - - -
380A SER* 2.5 28.0 + - - -
427A LEU* 3.6 1.4 - - - +
428A THR* 2.7 55.4 + - + +
430A VAL* 3.8 12.2 - - + +
450A MET* 3.5 26.0 - - + -
451A MET* 4.1 15.6 - - + +
503A HIS* 4.1 4.5 + - + -
504A VAL 3.5 7.6 - - - -
505A PHE* 3.3 37.9 - + + -
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Residues in contact with LEU 378 (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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376A ASN 3.4 11.4 - - - +
377A TYR* 1.3 84.4 - - - +
379A GLY* 1.3 59.0 + - - +
405A VAL* 3.4 23.4 - - + +
406A LYS* 5.9 7.6 - - + -
408A MET* 3.4 9.7 - - - +
409A GLN* 2.9 31.3 - - + +
427A LEU* 3.8 19.1 - - + -
428A THR* 5.6 1.8 - - - -
467A ILE* 5.1 4.7 - - + -
504A VAL* 2.8 30.7 + - + +
505A PHE 4.3 2.9 - - - +
506A GLU* 4.1 27.4 - - + +
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Residues in contact with GLY 379 (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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377A TYR* 3.1 28.8 - - - -
378A LEU* 1.3 79.8 - - - +
380A SER* 1.3 59.4 + - - -
405A VAL* 4.1 6.7 - - - -
408A MET* 4.5 8.3 - - - -
504A VAL* 3.1 27.9 + - - +
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Residues in contact with SER 380 (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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377A TYR* 2.5 23.5 + - - -
379A GLY* 1.3 74.7 + - - -
381A THR* 1.3 68.9 + - - +
404A ARG* 3.8 14.6 + - - -
405A VAL* 4.1 8.5 - - - +
408A MET* 4.5 4.4 - - - +
501A ILE* 4.1 12.3 - - - -
502A CYS 3.3 11.9 - - - -
503A HIS* 2.6 27.4 + - - -
504A VAL* 4.7 0.4 - - - +
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Residues in contact with THR 381 (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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380A SER* 1.3 84.4 - - - +
382A GLN* 1.3 61.6 + - - +
383A LEU* 5.1 1.4 - - + +
401A ALA* 3.1 44.8 - - + +
404A ARG* 2.8 41.5 + - - +
501A ILE* 3.6 4.5 - - - +
502A CYS* 2.9 34.0 + - + +
504A VAL* 4.8 0.9 - - + -
447B GLN* 4.1 9.4 - - - +
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Residues in contact with GLN 382 (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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381A THR* 1.3 74.4 + - - +
383A LEU* 1.3 62.4 + - - +
404A ARG* 5.0 1.0 - - - +
474A ARG* 3.4 36.2 - - - +
499A LYS* 3.3 16.6 - - + +
500A MET 3.0 20.6 - - - +
501A ILE* 3.7 15.7 - - + +
444B ALA 4.3 8.7 + - - +
445B ASP* 2.8 52.3 - - - +
446B THR* 3.8 3.8 - - - -
447B GLN* 3.0 28.7 + - - +
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Residues in contact with LEU 383 (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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381A THR* 5.1 1.6 - - + +
382A GLN* 1.3 74.2 - - - +
384A LEU* 1.3 81.3 + - - +
385A SER 4.2 0.4 - - - +
397A GLN* 3.8 50.3 - - + +
400A GLU* 6.2 0.9 - - + -
401A ALA* 4.7 5.4 - - + -
471A MET* 5.8 0.9 - - - -
499A LYS* 3.7 6.2 - - - +
500A MET* 3.0 49.2 + - + +
502A CYS* 4.1 22.9 - - - -
445B ASP 5.0 0.4 - - - -
446B THR* 3.9 13.0 - - - +
447B GLN* 4.7 7.6 - - + -
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Residues in contact with LEU 384 (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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383A LEU* 1.3 88.2 - - - +
385A SER* 1.3 61.6 + - - +
386A GLU* 4.8 1.9 - - - +
397A GLN* 4.6 4.0 + - - -
498A TYR* 3.3 22.4 - - + +
499A LYS* 4.1 9.0 - - + -
446B THR* 3.4 48.6 + - + +
448B GLU* 5.3 6.1 - - + -
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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