Contacts of the strand formed by residues 494 - 503 (chain A) in PDB entry 1IVV
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 THR 494 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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452A GLU* 3.7 0.7 - - - -
453A GLU* 3.0 37.2 + - - +
492A GLY 3.4 9.7 + - - +
493A ARG* 1.3 82.5 - - - +
495A TRP* 1.3 76.7 + - - +
513A LYS* 3.2 30.5 - - + +
514A LEU 3.4 13.9 - - - +
515A HIS* 3.6 32.3 - - + +
516A ALA 5.6 0.2 - - - +
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Residues in contact with TRP 495 (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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450A VAL* 4.3 8.7 - - + -
451A GLU 3.4 7.0 - - - +
452A GLU* 2.9 37.5 + - + +
477A LEU* 4.9 0.4 - - + -
485A ARG* 3.7 13.8 - - + +
486A GLU 3.5 23.1 - - - -
487A ALA* 4.1 20.9 - - + -
493A ARG* 3.7 22.9 - - + -
494A THR* 1.3 82.2 - - - +
496A ILE* 1.3 62.8 + - - +
497A ILE* 4.1 3.9 + - + +
512A TYR 3.9 0.7 - - - +
513A LYS* 3.5 0.3 - - - -
514A LEU* 2.8 50.6 + - + +
516A ALA* 4.1 23.1 - - + -
518A ASN* 4.9 0.4 - - - -
540A ASP* 4.3 11.7 - - + -
541A LEU* 3.7 46.7 - - + -
586A HIS* 4.9 3.6 - + - -
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Residues in contact with ILE 496 (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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449A ARG 3.6 0.5 - - - +
450A VAL* 3.2 4.8 - - - -
451A GLU* 2.8 53.2 + - + +
453A GLU* 3.5 22.4 - - + +
474A ARG* 3.4 44.0 - - + +
495A TRP* 1.3 76.5 - - - +
497A ILE* 1.3 72.6 + - - +
498A SER* 3.8 6.5 + - - +
511A GLY* 4.5 4.3 - - - -
512A TYR 3.4 16.6 - - - +
513A LYS* 4.0 23.8 - - + -
614A GLU* 4.3 10.8 - - + -
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Residues in contact with ILE 497 (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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441A MET* 3.7 36.1 - - + -
443A ILE* 3.6 22.5 - - + +
448A ASN* 4.1 8.5 - - + +
449A ARG 3.3 12.3 - - - +
450A VAL* 3.9 19.1 - - + -
495A TRP* 4.4 9.0 - - + +
496A ILE* 1.3 75.3 - - - +
498A SER* 1.3 58.8 + - - +
511A GLY* 3.2 2.1 - - - -
512A TYR* 3.0 37.9 + - + +
514A LEU* 4.6 7.0 - - + -
582A ILE* 4.5 0.7 - - + -
584A VAL* 4.2 12.6 - - + -
611A LEU* 3.6 31.4 - - + -
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Residues in contact with SER 498 (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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443A ILE* 4.4 4.7 - - - -
448A ASN* 3.2 6.9 - - - +
449A ARG* 2.7 72.5 + - - +
451A GLU* 4.1 5.1 + - - -
496A ILE* 3.8 9.6 + - - -
497A ILE* 1.3 75.5 - - - +
499A ASN* 1.3 61.2 + - - +
500A PRO* 3.5 1.1 - - - +
509A PRO* 4.4 7.2 - - - -
510A VAL 3.1 18.4 - - - -
511A GLY* 4.2 2.2 - - - -
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Residues in contact with ASN 499 (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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443A ILE* 2.8 30.5 + - + +
444A ASP* 3.3 21.4 + - - +
445A GLY* 4.2 3.6 + - - -
447A THR* 3.1 23.9 + - - +
448A ASN* 4.1 0.4 + - - -
498A SER* 1.3 73.9 - - - +
500A PRO* 1.3 62.1 - - - +
501A GLU* 3.0 19.8 + - - +
502A SER* 3.0 39.6 + - - +
509A PRO* 3.6 7.7 - - - +
510A VAL* 3.1 12.3 + - + -
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Residues in contact with PRO 500 (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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447A THR* 3.4 19.3 - - + +
448A ASN* 4.1 0.7 - - - -
449A ARG* 3.5 36.5 - - + +
498A SER 3.5 7.8 - - - +
499A ASN* 1.3 84.0 - - - +
501A GLU* 1.3 67.4 + - + +
502A SER 3.5 0.6 + - - -
503A LYS* 4.1 18.4 - - - -
509A PRO* 4.4 12.8 - - + +
578A ASP* 5.0 1.8 - - - +
579A GLY* 4.2 12.3 - - - -
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Residues in contact with GLU 501 (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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447A THR* 3.7 36.0 + - - +
499A ASN* 3.0 7.9 + - - +
500A PRO* 1.3 84.1 - - + +
502A SER* 1.3 59.8 - - - +
503A LYS* 4.0 5.7 + - - +
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Residues in contact with SER 502 (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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267A ARG* 5.8 0.3 + - - -
444A ASP* 2.5 32.9 + - - +
499A ASN* 3.0 35.0 + - - +
500A PRO 3.5 0.2 - - - -
501A GLU* 1.3 78.9 - - - +
503A LYS* 1.3 63.7 + - - +
509A PRO* 3.2 0.9 - - - +
510A VAL* 2.8 27.5 + - - +
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Residues in contact with LYS 503 (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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500A PRO 4.1 15.9 - - - +
501A GLU* 4.0 2.8 + - - +
502A SER* 1.3 82.4 + - - +
504A ASN* 1.3 65.5 + - - +
507A ASN* 3.1 47.6 + - - +
508A GLU 3.2 7.4 - - - +
509A PRO* 3.8 23.1 - - + -
510A VAL* 4.0 5.5 - - - +
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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