Contacts of the helix formed by residues 549 - 558 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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507A MET* 3.5 56.0 - - + +
508A ASN 5.8 0.2 - - - +
510A LEU* 3.8 11.0 - - + +
548A THR* 1.3 72.1 - - - +
550A GLU* 1.3 53.9 - - - +
552A LEU* 3.8 0.6 - - - +
553A GLN* 2.6 40.5 + - + +
487B ARG 4.4 13.8 - - - +
489B ARG* 4.1 19.5 - - - +
569B PRO* 4.1 23.3 - - + -
572B ARG* 4.5 9.0 - - + +
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Residues in contact with GLU 550 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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548A THR* 3.6 8.0 + - - +
549A VAL* 1.3 80.7 - - - +
551A GLN* 1.3 58.6 + - + +
553A GLN* 3.5 20.4 + - - +
554A LYS* 2.9 59.1 + - + +
489B ARG* 4.5 19.2 + - - +
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Residues in contact with GLN 551 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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546A ASN 4.3 2.1 - - - +
547A GLN* 3.6 29.2 + - + +
548A THR* 2.9 52.1 + - - +
550A GLU* 1.3 78.9 - - + +
552A LEU* 1.3 56.5 + - - +
554A LYS* 4.1 3.1 - - - +
555A MET* 2.9 35.1 + - - +
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Residues in contact with LEU 552 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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507A MET* 3.6 29.4 - - + -
510A LEU* 4.3 9.2 - - + -
513A CYS* 4.2 11.4 - - - -
539A ILE* 3.5 31.6 - - + -
544A VAL* 3.8 34.8 - - + -
547A GLN* 4.3 10.0 - - + +
548A THR 2.7 19.1 + - - +
549A VAL* 3.8 3.8 - - - +
551A GLN* 1.3 72.2 - - - +
553A GLN* 1.3 63.1 + - - +
555A MET* 3.5 12.6 - - + +
556A LEU* 3.0 35.0 + - + +
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Residues in contact with GLN 553 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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507A MET* 4.2 4.7 - - + +
549A VAL* 2.6 26.4 + - - +
550A GLU* 3.4 27.2 + - - +
552A LEU* 1.3 75.5 - - - +
554A LYS* 1.3 66.3 + - - +
557A ARG* 3.2 50.1 + - - +
489B ARG* 5.2 2.8 - - - +
531B HIS* 3.6 23.6 + - - -
572B ARG* 2.6 43.0 - - + +
574B PHE* 3.7 12.8 - - + -
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Residues in contact with LYS 554 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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550A GLU* 2.9 37.5 + - + +
551A GLN* 4.1 3.6 - - - +
553A GLN* 1.3 81.4 - - - +
555A MET* 1.3 63.6 + - - +
557A ARG* 3.2 5.2 + - - +
558A GLU* 2.8 56.7 + - - +
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Residues in contact with MET 555 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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539A ILE* 3.8 20.0 - - + +
542A ILE* 3.2 46.2 - - + +
547A GLN* 4.0 23.3 - - - -
551A GLN 2.9 19.6 + - - +
552A LEU* 3.5 16.6 - - + +
554A LYS* 1.3 78.6 - - - +
556A LEU* 1.3 63.8 + - - +
558A GLU* 3.3 4.7 + - - +
559A MET* 3.0 51.6 + - + +
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Residues in contact with LEU 556 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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495A LYS* 4.2 11.6 - - - +
501A MET* 4.1 19.9 - - + +
503A ILE* 5.8 0.4 - - + -
505A LEU* 3.4 32.3 - - + -
539A ILE* 3.8 26.2 - - + -
552A LEU* 3.0 15.4 + - + +
555A MET* 1.3 80.4 - - - +
557A ARG* 1.3 62.7 + - - +
558A GLU 3.5 0.2 + - - -
559A MET* 3.6 19.1 + - - +
563A ILE* 5.1 2.5 - - + +
565A PHE* 3.9 32.5 - - + -
574B PHE* 3.5 34.1 - - + -
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Residues in contact with ARG 557 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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495A LYS* 4.3 4.4 + - - +
553A GLN* 3.2 35.9 + - - +
554A LYS* 3.2 6.0 + - - +
556A LEU* 1.3 76.9 - - - +
558A GLU* 1.3 62.1 + - + +
560A ARG* 3.1 23.4 + - - -
703A SO4 3.4 19.6 + - - +
531B HIS* 4.5 4.6 + - - -
572B ARG* 3.9 10.9 - - - +
573B GLU 2.9 35.8 + - - +
574B PHE* 3.7 19.4 - - + +
702B SO4 2.9 39.2 + - - -
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Residues in contact with GLU 558 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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554A LYS* 2.8 50.9 + - - +
555A MET* 4.1 4.5 + - - +
557A ARG* 1.3 80.2 - - + +
559A MET* 1.3 64.4 + - - +
560A ARG* 3.5 12.7 + - - +
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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