Contacts of the helix formed by residues 549 - 558 (chain B) in PDB entry 1KWA
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 549 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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507B MET* 3.3 52.2 - - + +
547B GLN 3.9 0.8 + - - -
548B THR* 1.3 71.5 - - - +
550B GLU* 1.3 75.1 + - + +
552B LEU* 3.2 19.2 + - - +
553B GLN* 3.3 7.8 + - + +
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Residues in contact with GLU 550 (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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548B THR* 3.0 27.3 + - - +
549B VAL* 1.3 90.3 - - + +
551B GLN* 1.3 83.0 + - + +
552B LEU 3.1 2.6 + - - -
553B GLN* 3.3 3.8 + - - +
554B LYS* 3.3 15.6 + - - +
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Residues in contact with GLN 551 (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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548B THR* 3.6 12.4 + - - +
550B GLU* 1.3 99.3 + - + +
552B LEU* 1.3 63.0 + - - +
553B GLN 3.4 0.2 - - - -
554B LYS* 3.4 14.7 - - + +
555B MET* 3.1 25.3 + - - +
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Residues in contact with LEU 552 (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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507B MET* 3.1 22.4 - - + -
513B CYS* 4.7 6.5 - - + -
539B ILE* 4.4 5.0 - - + +
544B VAL* 3.1 58.8 - - + +
547B GLN* 4.1 12.3 - - + +
548B THR 3.2 19.3 + - - +
549B VAL* 3.2 10.5 + - - +
550B GLU 3.0 0.4 - - - -
551B GLN* 1.3 77.3 - - - +
553B GLN* 1.3 61.8 + - - +
555B MET* 3.1 50.7 - - + +
556B LEU* 3.8 4.2 + - - +
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Residues in contact with GLN 553 (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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507B MET* 4.0 19.0 - - - +
549B VAL* 3.3 8.7 + - + +
550B GLU* 4.1 5.6 - - - +
552B LEU* 1.3 75.7 - - - +
554B LYS* 1.3 68.7 + - - +
555B MET 3.0 2.4 + - - -
556B LEU* 3.3 17.4 + - + +
557B ARG* 3.6 12.4 + - + +
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Residues in contact with LYS 554 (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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550B GLU 3.3 7.4 + - - +
551B GLN* 3.4 26.9 - - + +
553B GLN* 1.3 79.4 - - - +
555B MET* 1.3 65.6 + - + +
557B ARG* 3.7 2.9 + - - +
558B GLU* 3.6 31.1 + - - +
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Residues in contact with MET 555 (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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539B ILE* 3.2 37.7 - - + -
542B ILE* 4.6 20.2 - - - -
547B GLN* 4.9 9.0 - - - +
551B GLN 3.1 15.0 - - - +
552B LEU* 3.1 33.2 - - + +
553B GLN 3.0 0.4 - - - -
554B LYS* 1.3 77.7 - - - +
556B LEU* 1.3 55.8 + - - +
558B GLU* 3.1 5.7 + - - +
559B MET* 2.6 55.5 + - + +
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Residues in contact with LEU 556 (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 LYS* 4.1 20.3 - - - +
501B MET* 3.6 32.2 - - + +
503B ILE* 5.0 0.9 - - + -
505B LEU* 4.2 25.4 - - + -
536B ILE* 5.3 0.7 - - + -
539B ILE* 3.9 27.6 - - + -
552B LEU 3.8 4.4 + - - +
553B GLN* 3.3 12.9 + - + +
555B MET* 1.3 79.1 - - - +
557B ARG* 1.3 62.0 + - - +
559B MET* 3.8 22.3 + - + +
563B ILE* 5.1 5.6 - - + -
565B PHE* 3.9 25.1 - - + -
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Residues in contact with ARG 557 (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 LYS* 4.6 4.9 + - - +
498B ASP* 4.1 7.2 - - - +
553B GLN* 3.6 11.5 + - + +
554B LYS* 4.3 6.5 - - - +
555B MET 3.4 0.8 - - - -
556B LEU* 1.3 78.6 - - - +
558B GLU* 1.3 63.3 + - + +
560B ARG* 2.9 22.3 + - - -
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Residues in contact with GLU 558 (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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554B LYS* 3.6 18.2 + - - +
555B MET* 3.1 6.5 + - - +
557B ARG* 1.3 81.6 - - + +
559B MET* 1.3 64.8 + - - +
560B ARG* 3.0 22.9 + - - +
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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