Contacts of the helix formed by residues 492 - 506 (chain B) in PDB entry 1U5T
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 PHE 492 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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434B ILE* 3.4 31.2 - - + -
478B VAL* 6.3 1.6 - - + -
480B VAL* 3.0 49.4 - - + -
484B ILE* 3.9 18.4 - - + -
486B CYS* 4.5 2.7 - - - -
488B THR* 5.1 4.2 - - + +
490B GLU 3.6 2.7 + - - -
491B LYS* 1.3 72.0 - - - +
493B ASP* 1.3 67.2 + - - +
495B VAL* 2.8 36.5 + - - +
496B LYS* 3.0 20.5 + - + -
531B ILE* 4.7 0.2 - - + -
535B VAL* 3.1 29.6 - - + -
538B ASN* 4.2 20.2 - - + -
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Residues in contact with ASP 493 (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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491B LYS* 4.1 8.8 - - + +
492B PHE* 1.3 86.3 + - - +
494B VAL* 1.3 56.5 + - + +
495B VAL 2.8 4.7 + - - -
496B LYS* 2.7 26.5 + - - +
497B GLU* 2.5 37.5 + - - +
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Residues in contact with VAL 494 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
432B TYR* 4.9 1.2 - - - -
490B GLU* 3.8 17.1 - - + +
491B LYS* 2.7 69.5 - - + +
493B ASP* 1.3 73.7 - - + +
495B VAL* 1.3 57.5 + - - +
497B GLU* 4.0 19.4 - - - +
498B LYS* 3.5 30.0 + - - +
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Residues in contact with VAL 495 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
432B TYR* 3.8 21.1 - - + -
434B ILE* 4.3 25.4 - - + -
488B THR* 4.8 3.1 - - - +
490B GLU* 4.0 16.8 - - + +
491B LYS 2.9 15.9 - - - +
492B PHE* 2.8 17.7 - - - +
494B VAL* 1.3 77.4 - - - +
496B LYS* 1.3 71.6 + - - +
497B GLU 3.1 0.9 - - - -
498B LYS* 3.3 6.2 + - - +
499B LEU* 3.1 16.3 + - - +
527B TRP* 3.2 36.0 - - + -
535B VAL* 6.1 0.9 - - + -
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Residues in contact with LYS 496 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
492B PHE* 3.0 19.0 + - + +
493B ASP* 2.7 28.4 + - - +
495B VAL* 1.3 78.3 - - - +
497B GLU* 1.3 57.0 + - - +
499B LEU* 2.6 31.1 + - - +
500B VAL* 3.0 20.2 + - + +
535B VAL* 4.8 11.1 - - + +
538B ASN* 3.4 24.5 + - + +
539B CYS* 4.0 41.3 - - + +
542B GLU* 4.3 16.5 + - + +
544B ASP* 4.0 14.8 - - - +
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Residues in contact with GLU 497 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
493B ASP 2.5 19.4 + - - +
494B VAL* 4.0 20.4 - - - +
496B LYS* 1.3 72.4 - - - +
498B LYS* 1.3 79.7 + - - +
499B LEU 2.6 2.6 + - - -
500B VAL* 3.0 8.0 + - - +
501B ASP* 2.9 41.9 + - - +
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Residues in contact with LYS 498 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
430B THR* 5.1 21.1 + - - +
432B TYR* 3.6 39.0 - - + +
490B GLU* 6.2 2.4 - - - +
494B VAL* 3.5 16.3 + - - +
495B VAL 3.3 9.1 + - - +
497B GLU* 1.3 92.7 + - - +
499B LEU* 1.3 63.6 + - - +
501B ASP* 4.1 5.6 - - - +
502B LEU* 3.2 21.0 + - - +
527B TRP* 6.1 0.4 - - + -
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Residues in contact with LEU 499 (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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495B VAL 3.1 9.1 + - - +
496B LYS* 2.6 20.5 + - - +
498B LYS* 1.3 68.0 - - - +
500B VAL* 1.3 74.3 + - + +
502B LEU* 2.7 22.4 + - + -
503B ILE* 2.6 42.6 + - + -
514B LEU* 3.7 11.9 - - + -
518B LEU* 5.1 3.1 - - + -
527B TRP* 4.0 25.3 - - + -
532B LEU* 3.5 29.4 - - + -
535B VAL* 4.1 14.8 - - + -
536B LEU* 4.6 6.1 - - + -
539B CYS* 5.6 2.2 - - - -
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Residues in contact with VAL 500 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
496B LYS* 3.4 30.5 - - + +
497B GLU* 3.3 7.6 - - - +
499B LEU* 1.3 81.9 - - + +
501B ASP* 1.3 63.1 + - - +
503B ILE* 2.5 26.2 + - - +
504B GLY* 2.6 11.0 + - - -
539B CYS* 5.0 3.6 - - - -
544B ASP* 4.1 24.9 - - + +
545B LEU* 4.1 15.3 - - + -
558B LYS* 3.6 37.9 - - + -
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Residues in contact with ASP 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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497B GLU* 2.9 33.6 + - - +
498B LYS* 4.1 5.8 - - - +
500B VAL* 1.3 85.7 - - - +
502B LEU* 1.3 57.1 + - - +
504B GLY* 3.2 3.5 + - - +
505B ASP* 3.0 30.7 + - - +
558B LYS* 4.0 22.4 + - - +
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Residues in contact with LEU 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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498B LYS 3.2 12.1 + - - +
499B LEU* 2.7 27.5 + - + +
501B ASP* 1.3 72.2 - - - +
503B ILE* 1.3 76.6 + - + +
505B ASP* 3.0 8.6 + - + +
506B ASN* 3.0 30.7 + - - +
514B LEU* 5.2 4.3 - - + -
517B ILE* 3.4 26.0 - - + -
518B LEU* 3.1 35.4 - - + -
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Residues in contact with ILE 503 (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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499B LEU* 2.6 24.0 + - + +
500B VAL* 2.5 13.7 + - - +
502B LEU* 1.3 76.8 - - - +
504B GLY* 1.3 68.6 + - - +
506B ASN* 2.7 29.3 + - - +
507B PRO* 3.3 0.8 - - + -
509B SER* 5.3 0.2 - - - -
514B LEU* 3.2 29.8 - - + -
536B LEU* 3.7 19.1 - - + -
545B LEU* 3.2 31.6 - - + -
556B TYR* 4.2 11.7 - - + +
557B TYR* 4.1 33.4 - - - +
558B LYS 4.5 0.2 - - - +
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Residues in contact with GLY 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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500B VAL 2.6 16.6 + - - -
501B ASP 3.4 6.3 - - - -
503B ILE* 1.3 74.5 - - - +
505B ASP* 1.3 66.2 + - - +
507B PRO* 3.0 19.1 - - - +
558B LYS* 4.0 28.2 - - - +
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Residues in contact with ASP 505 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
501B ASP* 3.0 18.8 + - - +
502B LEU* 3.0 11.4 + - + +
504B GLY* 1.3 72.6 - - - +
506B ASN* 1.3 68.5 + - - +
507B PRO* 2.8 13.0 - - - +
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Residues in contact with ASN 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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502B LEU* 3.3 26.2 + - + +
503B ILE* 2.7 17.5 + - - +
505B ASP* 1.3 81.7 - - - +
507B PRO* 1.3 67.2 - - - +
509B SER* 3.1 17.3 + - - +
513B ARG* 3.3 36.1 + - - +
514B LEU* 5.4 1.1 - - + +
517B ILE* 3.6 15.6 - - + +
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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