Contacts of the strand formed by residues 499 - 506 (chain B) 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 LYS 499 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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382B GLN* 4.1 21.0 + - - +
383B LEU 3.4 7.0 - - - +
384B LEU* 4.4 15.3 - - + -
473B ARG* 3.9 2.0 - - - +
474B ARG* 3.0 40.8 + - + +
497B GLN 4.4 0.2 - - - -
498B TYR* 1.3 72.3 - - - +
500B MET* 1.3 61.4 + - - +
501B ILE 4.0 0.4 - - - -
445C ASP* 3.0 42.4 + - - +
446C THR* 5.0 2.0 - - + -
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Residues in contact with MET 500 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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382B GLN* 4.4 1.1 - - - -
383B LEU* 3.0 45.3 + - + +
385B SER* 3.7 22.0 - - - +
394B ARG* 4.6 7.2 - - - +
459B SER* 3.0 29.8 - - - +
471B MET* 3.2 43.7 - - + +
472B ALA 3.6 1.3 - - - -
473B ARG* 3.0 44.0 - - - +
498B TYR* 3.6 6.7 + - + +
499B LYS* 1.3 72.5 - - - +
501B ILE* 1.3 61.9 + - - +
502B CYS* 3.6 2.1 + - - -
762E TYR* 3.8 8.7 - - - +
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Residues in contact with ILE 501 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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380B SER* 3.6 7.0 - - - -
381B THR* 3.1 48.0 - - - +
382B GLN* 3.4 23.7 - - + +
453B HIS* 5.2 6.7 - - + +
471B MET* 3.3 17.6 - - - -
472B ALA 3.4 17.5 + - - +
473B ARG 5.3 0.2 - - - -
474B ARG* 4.2 29.8 - - - +
499B LYS 4.0 2.2 + - - -
500B MET* 1.3 70.4 - - - +
502B CYS* 1.3 60.0 + - - +
503B HIS* 3.7 33.1 + - + +
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Residues in contact with CYS 502 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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380B SER* 3.1 23.3 - - - -
381B THR* 2.9 15.0 + - - +
383B LEU* 4.2 10.1 - - - -
398B ALA* 5.1 1.8 - - - -
401B ALA* 3.5 34.1 - - + -
469B VAL* 4.0 8.3 - - + -
470B LEU 3.2 10.5 - - - +
471B MET* 3.3 40.6 - - - -
500B MET 4.1 4.9 - - - -
501B ILE* 1.3 70.8 - - - +
503B HIS* 1.3 61.5 + - - +
504B VAL* 3.6 2.3 + - - +
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Residues in contact with HIS 503 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377B TYR* 4.0 6.7 + + + -
380B SER* 2.6 27.3 + - - +
441B VAL* 6.3 0.4 - - + -
451B MET* 3.5 28.9 - - + +
453B HIS* 3.2 29.6 + + - -
468B VAL 3.5 2.3 - - - +
469B VAL* 3.5 2.1 - - - -
470B LEU* 2.9 59.3 + - + +
472B ALA 5.7 0.2 - - - -
474B ARG* 5.8 1.8 - - - -
501B ILE* 3.7 26.2 + - + +
502B CYS* 1.3 71.6 - - - +
504B VAL* 1.3 61.0 + - - +
505B PHE* 3.6 24.0 - + + -
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Residues in contact with VAL 504 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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377B TYR* 3.4 9.9 - - - -
378B LEU* 3.2 31.5 + - + -
379B GLY 2.7 23.4 + - - +
401B ALA 4.0 2.9 - - - +
402B VAL* 3.9 42.2 - - + -
405B VAL* 3.9 18.4 - - + -
467B ILE* 4.0 6.5 - - + -
468B VAL 3.9 2.2 - - - -
469B VAL* 4.2 16.2 - - + -
502B CYS 4.0 7.0 - - - +
503B HIS* 1.3 76.6 - - - +
505B PHE* 1.3 74.4 + - - +
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Residues in contact with PHE 505 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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375B ALA* 4.0 11.9 - - + -
376B ASN 3.1 8.7 - - - +
377B TYR* 3.5 37.7 - + + -
378B LEU* 4.2 2.6 - - - +
430B VAL* 3.7 17.5 - - + -
432B LEU* 3.6 24.2 - - + -
441B VAL* 3.5 24.7 - - + -
451B MET* 5.5 0.9 - - - -
467B ILE* 2.9 28.6 - - - +
468B VAL* 3.1 40.3 + - + +
470B LEU* 4.6 13.7 - - + -
503B HIS* 3.6 28.7 - + + -
504B VAL* 1.3 76.9 - - - +
506B GLU* 1.3 64.2 + - - +
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Residues in contact with GLU 506 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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375B ALA* 3.2 1.4 - - - -
376B ASN* 2.6 58.3 + - + +
378B LEU* 4.3 11.5 - - + +
406B LYS* 5.4 4.0 + - - -
427B LEU* 4.0 11.4 - - - +
466B ASN* 3.3 36.7 + - + +
467B ILE* 4.2 9.9 - - + +
468B VAL* 4.8 0.4 - - - +
505B PHE* 1.3 79.0 - - - +
507B SER* 1.3 67.0 + - - +
508B GLU* 5.1 3.4 - - - +
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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