Contacts of the strand formed by residues 453 - 462 (chain B) in PDB entry 3IN5
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 GLY 453 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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452B LYS* 1.3 72.8 - - - +
454B ARG* 1.3 63.5 + - - -
455B THR 3.8 0.9 - - - -
477B VAL* 4.2 1.3 - - - -
478B VAL* 2.8 36.2 + - - +
513B ILE* 3.8 15.4 - - - +
514B SER 3.7 6.1 - - - -
515B SER 3.3 13.0 - - - -
516B PHE* 3.7 8.8 - - - -
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Residues in contact with ARG 454 (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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453B GLY* 1.3 77.3 - - - +
455B THR* 1.3 59.4 + - - +
456B VAL* 4.1 3.2 + - - -
472B SER 3.9 0.7 - - - +
473B THR* 3.0 7.1 + - - +
474B VAL* 2.7 61.9 + - + +
475B SER* 4.1 9.4 + - - +
476B SER 3.4 25.8 - - - +
477B VAL* 4.3 5.6 - - + -
478B VAL* 6.2 0.4 - - - -
487B ILE* 5.1 1.8 - - - +
515B SER* 3.1 31.4 + - - +
516B PHE 6.0 1.6 - - - -
517B PRO* 5.8 4.0 - - + -
4Q G 4.4 1.4 + - - -
5Q G 2.9 39.2 + - - -
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Residues in contact with THR 455 (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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453B GLY 3.8 0.4 - - - -
454B ARG* 1.3 75.0 - - - +
456B VAL* 1.3 62.5 + - - +
457B THR* 4.9 1.6 - - - +
471B ALA* 4.9 6.7 - - + -
472B SER 3.4 10.3 - - - +
473B THR* 3.2 27.2 + - - +
512B ARG 3.4 1.6 - - - +
513B ILE* 3.3 4.3 - - - -
514B SER* 2.9 45.9 + - - +
515B SER* 2.4 35.7 + - - -
5Q G 5.5 1.8 - - + -
6Q A 3.3 12.8 - - - +
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Residues in contact with VAL 456 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
453B GLY 6.1 0.2 - - - +
454B ARG 4.1 1.7 + - - +
455B THR* 1.3 75.6 - - - +
457B THR* 1.3 65.7 + - - +
471B ALA* 3.5 0.9 - - - +
472B SER 3.0 29.3 + - - +
478B VAL* 5.3 3.4 - - + -
484B ILE* 4.2 25.4 - - + -
487B ILE* 3.7 37.5 - - + -
488B ALA* 4.2 20.2 - - + +
491B LEU* 3.6 4.7 - - + +
511B VAL* 4.0 24.5 - - + -
512B ARG 3.2 7.0 - - - +
513B ILE* 4.9 9.2 - - + -
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Residues in contact with THR 457 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
455B THR* 4.4 5.7 + - - +
456B VAL* 1.3 77.9 - - - +
458B ILE* 1.3 70.9 + - - +
459B LYS* 4.1 0.5 + - - +
469B THR* 4.1 13.2 - - - +
470B ARG 3.0 21.3 - - - +
471B ALA* 3.4 20.5 - - + +
491B LEU* 4.6 0.4 - - - -
511B VAL* 3.5 1.6 - - - -
512B ARG* 2.7 52.2 + - - +
514B SER* 4.4 6.8 + - - -
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Residues in contact with ILE 458 (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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435B CYS* 5.0 4.0 - - - -
456B VAL* 5.4 0.4 - - + -
457B THR* 1.3 75.8 - - - +
459B LYS* 1.3 62.3 + - - +
460B LEU* 4.0 26.0 - - + -
469B THR* 3.2 26.9 - - - -
470B ARG* 2.9 28.0 + - + +
488B ALA* 4.1 33.9 - - + +
491B LEU* 3.6 16.6 - - + +
492B LEU* 3.4 37.9 - - + +
509B MET* 5.9 2.9 - - + -
510B GLY 3.4 9.0 - - - +
511B VAL* 4.6 7.2 - - + -
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Residues in contact with LYS 459 (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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419B GLU* 3.0 41.5 + - - -
457B THR 5.5 0.4 - - - +
458B ILE* 1.3 72.3 - - - +
460B LEU* 1.3 64.2 - - - +
461B LYS* 4.7 9.1 - - - +
467B VAL* 3.9 25.9 - - + +
468B LYS 3.9 3.4 - - - -
469B THR* 3.9 11.7 - - + -
508B LEU* 3.8 19.0 - - + +
509B MET* 3.1 10.7 - - - +
510B GLY* 2.7 45.3 + - - +
512B ARG* 6.0 3.6 - - - +
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Residues in contact with LEU 460 (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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458B ILE* 4.0 21.5 - - + -
459B LYS* 1.3 79.5 - - - +
461B LYS* 1.3 61.3 + - - +
467B VAL* 3.3 7.2 - - - +
468B LYS* 3.1 60.2 + - + +
470B ARG* 5.6 1.1 - - + +
492B LEU* 3.5 27.4 - - + -
495B GLU* 3.9 32.1 - - + -
504B LEU* 4.9 6.1 - - + -
506B LEU* 4.0 24.5 - - + -
508B LEU 3.8 1.8 - - - -
509B MET* 4.0 10.1 - - + -
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Residues in contact with LYS 461 (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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419B GLU* 5.5 0.6 + - - -
421B THR* 4.4 4.5 + - - -
459B LYS* 4.7 8.7 - - - +
460B LEU* 1.3 75.5 - - - +
462B ASN* 1.3 65.0 + - - +
465B PHE* 3.9 22.6 - - + +
466B GLU 3.2 12.8 - - - +
467B VAL* 3.6 21.0 - - + +
468B LYS* 5.1 0.2 - - - -
506B LEU* 3.4 10.7 - - - +
507B ARG* 2.8 43.6 + - + +
508B LEU* 3.0 50.4 + - + +
5U 8OG 4.6 14.0 + - - -
6U G 5.7 0.2 + - - -
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Residues in contact with ASN 462 (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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461B LYS* 1.3 76.4 - - - +
463B VAL* 1.3 58.4 + - - +
464B ASN* 3.1 21.4 - - + +
465B PHE 3.2 17.3 + - - +
466B GLU* 3.2 42.0 + - + +
468B LYS* 3.3 23.6 + - - -
505B ARG* 3.2 14.6 + - + +
506B LEU* 5.1 0.9 - - - +
507B ARG* 3.2 13.7 - - - -
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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