Contacts of the helix formed by residues 643 - 653 (chain B) in PDB entry 1K2P
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 THR 643 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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513B GLU* 3.4 24.0 - - - +
577B LYS* 4.4 11.9 - - - +
580B ILE* 4.1 2.5 - - - -
642B PRO* 1.3 78.6 - - - +
644B PHE* 1.3 61.5 + - - +
645B LYS* 3.0 7.9 + - - +
646B ILE* 3.2 32.5 + - + +
647B LEU* 2.8 28.2 + - - +
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Residues in contact with PHE 644 (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 CYS* 3.5 17.5 - - - +
509B MET* 3.3 59.0 - - + -
510B GLU* 3.5 23.3 - - + +
513B GLU* 3.0 31.2 + - + +
522B LEU* 4.5 0.2 - - + -
576B SER 5.0 2.5 - - - -
579B ASP* 3.6 31.4 - - + -
580B ILE* 3.6 19.3 - - + +
583B PHE* 3.5 28.3 - + + -
643B THR* 1.3 71.9 - - - +
645B LYS* 1.3 54.6 + - - +
647B LEU* 3.8 6.7 - - + -
648B LEU* 2.8 34.7 + - - +
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Residues in contact with LYS 645 (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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510B GLU* 3.3 36.9 + - + +
513B GLU* 3.5 9.3 + - - +
643B THR* 3.0 9.8 - - - +
644B PHE* 1.3 79.4 - - - +
646B ILE* 1.3 65.0 - - + +
648B LEU* 3.4 16.8 + - - +
649B SER* 3.2 24.8 + - - +
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Residues in contact with ILE 646 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
642B PRO* 4.0 18.8 - - + -
643B THR* 3.2 30.6 + - + +
645B LYS* 1.3 75.6 - - + +
647B LEU* 1.3 67.0 + - - +
649B SER* 2.9 18.4 + - - -
650B ASN* 3.0 37.3 + - - +
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Residues in contact with LEU 647 (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 CYS* 3.8 7.0 - - - -
580B ILE* 3.8 30.1 - - + -
583B PHE* 3.6 35.0 - - + -
629B ILE* 4.1 17.2 - - + +
632B SER* 3.8 13.0 - - - +
633B CYS* 4.0 11.9 - - - -
642B PRO* 3.6 24.7 - - + -
643B THR 2.8 12.9 + - - +
644B PHE* 3.6 10.8 - - + +
646B ILE* 1.3 77.4 - - + +
648B LEU* 1.3 60.6 + - - +
650B ASN* 4.1 7.0 - - - +
651B ILE* 3.2 30.1 + - - +
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Residues in contact with LEU 648 (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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503B LYS* 4.3 9.9 - - + +
506B CYS* 3.7 19.9 - - + -
507B GLU* 3.8 32.1 - - + +
510B GLU* 3.3 32.5 - - + +
644B PHE 2.8 18.1 + - - +
645B LYS* 3.4 18.6 - - - +
647B LEU* 1.3 75.1 - - - +
649B SER* 1.3 64.2 + - - +
651B ILE* 3.4 4.8 + - + +
652B LEU* 3.1 45.8 + - + +
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Residues in contact with SER 649 (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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645B LYS* 3.2 20.2 + - - +
646B ILE* 2.9 11.5 + - - -
648B LEU* 1.3 77.7 - - - +
650B ASN* 1.3 62.1 - - - -
652B LEU* 2.8 26.9 + - - +
653B ASP* 3.3 19.7 + - - +
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Residues in contact with ASN 650 (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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629B ILE* 4.0 20.2 - - + +
642B PRO* 6.2 0.2 - - - +
646B ILE* 3.0 32.9 + - - +
647B LEU* 4.1 9.6 - - - +
649B SER* 1.3 78.1 - - - +
651B ILE* 1.3 59.7 + - - +
653B ASP* 3.4 16.1 + - - +
654B VAL* 2.9 21.5 - - - +
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Residues in contact with ILE 651 (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* 3.4 36.4 - - + +
502B CYS* 4.0 28.7 - - + +
503B LYS* 4.2 23.6 - - + -
506B CYS* 4.5 4.9 - - + -
583B PHE* 4.1 22.0 - - + -
587B MET* 4.4 6.5 - - - -
629B ILE* 4.2 18.2 - - + -
647B LEU 3.2 19.4 + - - +
648B LEU* 3.7 7.6 - - + +
649B SER 3.1 0.6 - - - -
650B ASN* 1.3 77.2 - - - +
652B LEU* 1.3 66.4 + - + +
653B ASP 3.2 0.9 + - - -
654B VAL* 3.3 18.7 + - - +
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Residues in contact with LEU 652 (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* 6.0 1.6 - - + -
503B LYS* 4.0 31.0 - - + -
507B GLU* 5.6 0.2 - - - +
648B LEU* 3.1 43.8 + - + +
649B SER* 2.8 14.7 + - - +
651B ILE* 1.3 79.6 - - + +
653B ASP* 1.3 57.8 + - + +
654B VAL 3.8 1.4 + - - -
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Residues in contact with ASP 653 (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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625B LYS* 4.8 6.4 - - - +
649B SER* 3.3 22.0 + - - +
650B ASN* 3.6 10.8 - - - +
651B ILE 3.2 0.8 - - - -
652B LEU* 1.3 81.0 - - - +
654B VAL* 1.3 59.0 + - - +
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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