Contacts of the helix formed by residues 505 - 520 (chain B) in PDB entry 5TQW
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 505 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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494B TYR* 3.6 7.4 - - - -
498B MET* 4.7 9.1 - - + +
503B SER 3.6 2.9 + - - +
504B SER* 1.3 80.1 + - - +
506B LYS* 1.3 56.7 + - - +
507B MET 3.0 5.8 - - - -
508B LEU* 3.0 43.5 + - + +
509B LYS* 3.3 21.2 + - + +
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Residues in contact with LYS 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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504B SER* 3.3 30.1 + - - +
505B GLU* 1.3 78.5 - - - +
507B MET* 1.3 67.4 + - - +
508B LEU 3.3 0.2 - - - -
509B LYS* 4.5 7.6 - - - +
510B ALA* 2.7 39.3 + - - +
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Residues in contact with MET 507 (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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494B TYR* 3.4 24.9 - - + +
503B SER* 3.7 10.3 - - - +
504B SER 3.5 11.7 - - - +
505B GLU 3.0 0.4 - - - -
506B LYS* 1.3 92.2 - - + +
508B LEU* 1.3 59.9 + - - +
510B ALA* 3.9 4.9 - - + -
511B TRP* 2.9 75.5 + - + +
514B MET* 6.1 0.4 - - + -
645B LYS 5.6 0.2 - - - +
646B ARG* 5.6 2.0 - - - -
649B GLU* 3.7 38.1 - - + -
653B LEU* 5.9 0.9 - - + -
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Residues in contact with LEU 508 (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 LEU* 4.1 21.6 - - + +
494B TYR* 3.6 30.4 - - + -
495B SER* 5.2 7.2 - - - +
498B MET* 5.7 5.8 - - + -
505B GLU* 3.0 26.4 + - + +
507B MET* 1.3 77.5 - - - +
509B LYS* 1.3 62.9 + - + +
511B TRP* 3.0 4.9 + - - +
512B LYS* 2.8 35.5 + - + +
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Residues in contact with LYS 509 (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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505B GLU* 3.3 23.8 + - + +
506B LYS* 4.5 6.1 - - - +
508B LEU* 1.3 79.9 - - + +
510B ALA* 1.3 60.6 + - - +
512B LYS* 3.6 11.0 - - + +
513B GLU* 2.9 42.1 + - + +
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Residues in contact with ALA 510 (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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506B LYS 2.7 23.4 + - - +
507B MET* 3.5 13.5 - - + +
509B LYS* 1.3 77.0 - - - +
511B TRP* 1.3 65.3 + - + +
513B GLU* 3.1 11.2 + - - +
514B MET* 2.9 35.9 + - + +
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Residues in contact with TRP 511 (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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487B ILE* 4.2 13.5 - - + +
490B ASP* 3.3 36.6 - - + -
491B LEU* 3.7 25.6 - - + -
494B TYR* 3.5 33.2 - + + -
497B GLN* 5.5 0.4 - - - -
507B MET* 2.9 54.4 + - + +
508B LEU 3.8 2.2 - - - +
510B ALA* 1.3 76.6 - - + +
512B LYS* 1.3 62.3 + - - +
513B GLU 3.4 0.2 - - - -
514B MET* 3.4 35.6 - - + +
515B GLU* 2.9 30.4 + - - +
646B ARG* 3.6 33.1 - - + +
649B GLU* 5.8 0.4 - - + -
650B ILE* 5.6 6.1 - - + -
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Residues in contact with LYS 512 (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 LEU* 5.1 12.6 - - + -
508B LEU* 2.8 24.7 + - + +
509B LYS* 3.6 10.3 - - + +
511B TRP* 1.3 77.1 - - - +
513B GLU* 1.3 58.9 + - + +
515B GLU* 3.1 25.2 + - - +
516B GLU* 2.8 42.8 + - - +
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Residues in contact with GLU 513 (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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509B LYS* 2.9 27.9 + - + +
510B ALA* 3.1 6.8 + - - +
512B LYS* 1.3 73.7 - - + +
514B MET* 1.3 60.1 + - - +
516B GLU* 3.3 21.6 + - - +
517B LYS* 2.9 40.1 + - - +
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Residues in contact with MET 514 (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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483B PHE* 4.3 12.4 - - + -
487B ILE* 4.5 2.7 - - + -
507B MET* 6.1 0.4 - - + -
510B ALA* 2.9 19.9 + - + +
511B TRP* 3.4 42.6 - - + +
513B GLU* 1.3 76.2 - - - +
515B GLU* 1.3 57.5 + - - +
517B LYS* 3.1 7.7 + - - +
518B ALA* 2.9 24.6 + - - +
642B MET* 3.5 63.0 - - + +
645B LYS* 4.6 13.9 - - + +
646B ARG* 3.8 25.6 - - + +
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Residues in contact with GLU 515 (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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484B HIS* 3.1 35.2 - - + +
487B ILE* 3.3 41.1 - - + +
488B GLN* 5.7 1.9 - - - +
491B LEU* 4.3 5.2 - - - +
511B TRP 2.9 16.6 + - - +
512B LYS* 3.1 29.1 + - + +
514B MET* 1.3 75.8 - - - +
516B GLU* 1.3 58.3 + - + +
518B ALA* 3.0 9.5 + - + +
519B ILE* 2.9 35.2 + - + +
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Residues in contact with GLU 516 (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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512B LYS* 2.8 29.0 + - + +
513B GLU* 3.5 25.1 - - - +
514B MET 3.2 0.2 - - - -
515B GLU* 1.3 74.3 - - + +
517B LYS* 1.3 63.9 + - + +
519B ILE* 3.2 20.8 + - + -
520B HIS* 3.0 42.3 + - + +
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Residues in contact with LYS 517 (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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513B GLU* 2.9 25.1 + - - +
514B MET 3.3 7.4 - - - +
516B GLU* 1.3 77.3 - - + +
518B ALA* 1.3 60.8 + - - +
520B HIS* 3.2 10.5 + - + +
521B TYR* 3.1 36.3 - - + +
638B THR* 6.0 1.4 - - + +
642B MET* 3.7 43.0 - - + +
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Residues in contact with ALA 518 (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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480B LEU* 3.4 53.4 - - + +
483B PHE* 4.7 16.8 - - + -
484B HIS* 5.7 3.8 - - + +
487B ILE* 5.2 1.1 - - + -
514B MET 2.9 12.2 + - - +
515B GLU* 3.0 17.7 + - + +
517B LYS* 1.3 76.1 - - - +
519B ILE* 1.3 62.5 + - - +
521B TYR 4.3 0.3 + - - -
639B VAL* 6.2 0.9 - - + -
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Residues in contact with ILE 519 (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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480B LEU* 5.4 0.3 - - - +
515B GLU* 2.9 20.0 + - + +
516B GLU* 3.3 31.6 - - + +
517B LYS 3.2 0.4 - - - -
518B ALA* 1.3 78.8 - - - +
520B HIS* 1.3 72.1 + - + +
521B TYR 2.8 13.0 + - - -
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Residues in contact with HIS 520 (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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516B GLU* 3.0 40.0 + - + +
517B LYS* 3.2 15.6 + - + +
519B ILE* 1.3 93.5 - - + +
521B TYR* 1.3 77.8 + - + +
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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