Contacts of the strand formed by residues 508 - 517 (chain A) in PDB entry 3HS0
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 GLU 508 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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416A GLN* 3.2 29.7 + - + +
419A SER* 2.3 34.6 + - - -
421A ASN* 3.0 31.3 + - - +
450A SER* 5.0 0.2 + - - -
502A TYR 4.1 0.2 - - - +
503A GLN* 3.3 7.3 - - - +
504A VAL* 2.9 48.2 + - + +
507A ASN* 1.3 83.0 - - + +
509A ILE* 1.3 65.9 + - - +
510A VAL* 4.2 12.6 + - + +
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Residues in contact with ILE 509 (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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2A LEU* 4.5 15.0 - - + -
4A THR* 4.4 11.9 - - + -
413A TYR* 4.1 0.7 + - - -
416A GLN* 3.1 9.2 + - - +
501A TYR* 3.8 33.9 - - + -
502A TYR 3.8 2.5 - - - -
503A GLN* 4.6 1.3 - - + -
507A ASN 4.1 2.0 + - - +
508A GLU* 1.3 78.8 - - - +
510A VAL* 1.3 69.4 + - - +
511A ALA 4.6 0.4 - - - +
595A ASN* 3.2 28.9 + - + +
599A PHE* 4.4 16.4 - - + -
606A LEU* 4.4 10.1 - - + -
608A THR* 3.9 28.0 - - + -
612A LEU* 4.2 21.3 - - + +
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Residues in contact with VAL 510 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
413A TYR* 3.9 11.2 - - + +
421A ASN* 3.4 34.5 - - + +
422A TYR* 3.6 4.3 - - - -
423A LEU* 3.6 28.8 - - + +
501A TYR* 3.1 19.7 - - - +
502A TYR* 3.0 48.7 + - + +
504A VAL* 5.3 0.2 - - + -
508A GLU* 4.2 15.5 - - + +
509A ILE* 1.3 77.8 - - - +
511A ALA* 1.3 62.4 + - - +
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Residues in contact with ALA 511 (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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333A LYS* 5.6 0.7 - - - -
413A TYR* 3.4 19.2 + - - +
423A LEU* 3.6 10.1 - - - +
499A VAL* 5.6 0.4 - - + -
500A ALA 3.5 5.2 - - - +
501A TYR* 4.0 5.4 - - + -
509A ILE* 4.2 1.8 - - + -
510A VAL* 1.3 74.6 - - - +
512A ASP* 1.3 66.0 + - - +
595A ASN* 4.2 4.7 - - - +
598A VAL* 3.7 28.1 - - + +
599A PHE* 3.4 33.4 - - + -
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Residues in contact with ASP 512 (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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333A LYS* 2.8 39.6 + - - -
423A LEU* 3.6 22.7 - - + +
425A VAL* 3.0 34.4 + - + +
498A PHE 4.0 0.3 - - - +
499A VAL* 3.5 2.9 - - - +
500A ALA* 2.9 34.5 + - - +
511A ALA* 1.3 77.3 - - - +
513A SER* 1.3 72.4 + - - +
514A VAL* 4.4 0.7 - - - +
591A SER* 3.4 13.3 + - - -
598A VAL* 3.8 9.0 - - - -
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Residues in contact with SER 513 (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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329A PRO* 5.6 0.7 - - - +
333A LYS* 5.2 0.5 + - - -
425A VAL* 5.5 0.7 - - - -
497A ARG* 5.5 4.8 + - - -
498A PHE 3.1 11.2 - - - -
499A VAL* 3.8 18.8 - - - -
512A ASP* 1.3 83.1 + - - +
514A VAL* 1.3 73.7 + - - +
590A GLY* 3.4 8.1 - - - -
591A SER* 3.0 37.2 + - - +
598A VAL* 3.9 11.9 + - - +
601A ASP* 5.6 0.9 - - - +
602A ALA* 4.4 9.0 + - - +
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Residues in contact with VAL 514 (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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329A PRO* 5.9 5.6 - - + -
339A GLU* 5.6 2.9 - - - +
375A LYS* 6.3 0.9 - - - +
424A HIS* 5.8 1.3 - - + -
425A VAL* 3.6 37.5 - - + +
426A ALA* 5.3 1.1 - - - -
427A ILE* 4.3 19.7 - - + +
497A ARG* 3.6 4.3 - - - -
498A PHE* 2.9 34.5 + - + +
512A ASP* 4.4 2.2 - - - +
513A SER* 1.3 84.9 - - - +
515A TRP* 1.3 71.4 + - - +
516A VAL* 3.8 14.9 + - + +
589A ALA 4.3 5.2 - - - -
590A GLY* 5.1 0.9 - - - -
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Residues in contact with TRP 515 (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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327A LYS* 3.7 55.1 - - + +
495A SER* 3.3 34.8 + - - -
496A PHE 3.9 4.9 - - - -
497A ARG* 3.9 40.1 - - + +
514A VAL* 1.3 76.9 - - - +
516A VAL* 1.3 66.6 + - - +
517A ASP* 3.7 27.1 - - + -
581A GLU* 4.2 14.6 + - - -
584A ASP* 4.8 1.2 + - - -
589A ALA* 3.4 32.8 + - + +
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Residues in contact with VAL 516 (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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427A ILE* 4.2 15.3 - - + -
432A ILE* 3.5 29.2 - - + -
438A LEU* 4.5 2.2 - - + -
495A SER* 3.2 6.3 - - - -
496A PHE* 2.8 84.1 + - + +
498A PHE* 4.9 1.6 - - + -
514A VAL* 3.9 21.8 - - + +
515A TRP* 1.3 82.2 - - - +
517A ASP* 1.3 63.4 + - - +
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Residues in contact with ASP 517 (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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327A LYS* 4.6 8.6 - - - -
371A ASP* 4.0 21.0 - - - +
432A ILE* 3.6 22.7 + - - +
494A PRO 2.9 12.8 - - - +
495A SER* 4.1 5.8 - - - -
515A TRP* 3.7 30.4 + - + -
516A VAL* 1.3 76.7 - - - +
518A VAL* 1.3 79.2 + - - +
520A ASP* 4.1 2.1 - - - +
581A GLU* 4.9 1.2 - - - +
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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