Contacts of the strand formed by residues 491 - 495 (chain B) in PDB entry 1T9A
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 VAL 491 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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484B ALA* 3.9 24.2 - - + +
485B ASN* 5.1 2.5 - - - +
487B THR* 4.4 0.2 - - - +
489B ARG 3.4 16.1 + - - +
490B HIS* 1.3 78.7 - - - +
492B ILE* 1.3 64.1 + - - +
493B VAL* 4.1 20.8 - - + +
508B TRP* 4.1 15.9 - - + +
512B ASN* 5.8 0.4 + - - -
515B THR* 3.3 26.4 - - - +
543B LEU* 3.4 22.9 - - + +
545B ILE* 4.3 11.9 - - + -
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Residues in contact with ILE 492 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152B ALA* 4.0 14.4 - - + -
490B HIS* 3.9 18.8 - - + +
491B VAL* 1.3 77.0 - - - +
493B VAL* 1.3 69.1 + - - +
494B THR* 4.9 0.7 - - + -
514B HIS 4.3 7.9 - - - +
515B THR* 3.5 11.9 - - - +
517B ILE* 3.7 28.0 - - + -
535B ALA* 4.3 13.2 - - + +
539B LYS* 3.7 36.3 - - + -
542B SER* 4.1 7.9 - - - +
543B LEU 3.0 7.2 + - - +
544B VAL* 3.4 13.8 - - + +
545B ILE* 2.9 26.2 + - - +
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Residues in contact with VAL 493 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
491B VAL* 4.1 7.2 - - + -
492B ILE* 1.3 79.9 - - - +
494B THR* 1.3 69.2 + - - +
495B THR* 4.2 7.9 - - + -
504B ALA* 5.3 0.2 - - + -
508B TRP* 3.8 37.9 - - + +
510B TRP* 4.0 20.9 - - + -
515B THR 2.6 16.7 + - - +
516B PHE* 3.4 4.5 - - + -
517B ILE* 2.7 32.9 + - - +
545B ILE* 3.3 10.5 - - + +
547B ILE* 4.0 21.1 - - + -
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Residues in contact with THR 494 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
492B ILE* 4.9 0.7 - - + -
493B VAL* 1.3 78.9 - - - +
495B THR* 1.3 69.4 + - - +
517B ILE* 3.2 30.3 - - + -
528B GLY* 3.2 13.6 + - - -
531B ALA* 4.0 9.0 - - + +
532B ALA* 3.5 28.5 - - + +
535B ALA* 4.8 0.4 - - + -
544B VAL* 4.5 6.5 - - + -
545B ILE 2.8 7.8 + - - +
546B ASP* 3.1 25.1 - - - +
547B ILE 2.8 23.7 + - - -
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Residues in contact with THR 495 (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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493B VAL* 4.2 4.7 - - + -
494B THR* 1.3 83.9 - - - +
496B GLY* 1.3 68.9 + - - +
501B GLN* 3.5 12.6 - - - +
504B ALA* 4.0 19.1 - - + -
516B PHE* 3.8 25.6 - - + -
517B ILE 3.6 4.8 + - - -
518B THR* 2.8 26.0 + - - -
519B SER 5.1 0.2 + - - -
527B TYR* 3.9 13.7 - - - -
528B GLY* 3.2 19.3 + - - -
546B ASP* 3.7 1.3 - - - -
547B ILE* 3.0 15.9 - - + +
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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