Contacts of the helix formed by residues 602 - 612 (chain A) 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 602 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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562A ARG* 4.2 4.5 - - - +
600A ARG 5.3 0.9 - - - +
601A PHE* 1.3 80.7 - - - +
603A ASN* 1.3 63.4 + - - +
604A SER* 2.9 21.9 + - - -
605A GLU* 3.0 27.0 + - - +
606A THR* 2.7 29.2 + - - -
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Residues in contact with ASN 603 (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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558A LYS* 2.9 34.5 - - - +
559A PHE 3.8 4.2 + - - -
561A VAL* 3.5 36.3 - - + +
562A ARG* 3.4 23.8 + - - +
602A THR* 1.3 73.5 - - - +
604A SER* 1.3 58.5 + - - +
606A THR* 3.8 6.0 - - - -
607A ALA* 3.5 16.3 + - - +
436B SER 5.4 1.7 - - - +
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Residues in contact with SER 604 (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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602A THR* 3.0 18.2 + - - -
603A ASN* 1.3 78.5 - - - +
605A GLU* 1.3 64.5 + - - +
606A THR 3.3 0.2 - - - -
607A ALA* 3.4 7.0 + - - +
608A GLU* 3.2 28.1 + - - +
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Residues in contact with GLU 605 (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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600A ARG 3.9 4.5 - - - +
601A PHE* 3.4 22.9 - - + -
602A THR* 3.0 39.9 + - - +
604A SER* 1.3 76.3 + - - +
606A THR* 1.3 54.9 + - - +
608A GLU* 3.1 19.1 + - - +
609A HIS* 2.7 36.2 + - - +
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Residues in contact with THR 606 (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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561A VAL* 4.5 9.2 - - + +
562A ARG* 3.1 33.9 + - - +
598A TYR* 3.4 36.7 - - + +
601A PHE* 3.4 11.3 - - - +
602A THR 2.7 22.5 + - - -
603A ASN* 3.8 8.2 - - - -
605A GLU* 1.3 78.2 - - - +
607A ALA* 1.3 55.8 + - - +
609A HIS* 3.3 7.1 + - - +
610A ILE* 3.0 34.6 + - + +
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Residues in contact with ALA 607 (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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561A VAL* 4.7 1.5 - - + +
569A LEU* 3.9 31.6 - - + +
603A ASN 3.5 11.5 + - - +
604A SER* 3.4 11.1 + - - +
605A GLU 3.2 0.2 - - - -
606A THR* 1.3 80.4 - - - +
608A GLU* 1.3 57.5 - - + +
610A ILE* 3.5 3.5 + - - +
611A ALA* 3.0 27.0 + - - +
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Residues in contact with GLU 608 (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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604A SER* 3.2 15.0 + - - +
605A GLU* 3.1 25.7 + - - +
607A ALA* 1.3 76.1 - - + +
609A HIS* 1.3 59.7 + - - +
611A ALA* 3.0 23.3 + - - +
612A GLN* 3.0 22.3 + - + +
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Residues in contact with HIS 609 (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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598A TYR* 3.7 22.6 - + - -
601A PHE* 3.2 35.0 - + + -
605A GLU 2.7 20.2 + - - +
606A THR* 3.3 6.7 + - - +
608A GLU* 1.3 72.2 - - - +
610A ILE* 1.3 62.8 + - - +
612A GLN* 3.2 19.2 + - - +
614A LEU* 3.1 71.1 + - + +
615A ARG 3.4 14.9 + - - -
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Residues in contact with ILE 610 (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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561A VAL 5.2 2.0 - - - +
562A ARG 5.9 1.1 - - - +
564A SER 3.9 13.2 - - - +
566A PRO* 3.8 35.4 - - + -
569A LEU* 4.5 9.2 - - + -
581A TRP* 3.2 29.8 - - + +
598A TYR* 3.9 22.2 - - + +
606A THR* 3.0 24.0 + - + +
607A ALA* 3.9 5.8 - - - +
609A HIS* 1.3 75.0 - - + +
611A ALA* 1.3 59.3 + - - +
612A GLN 3.0 0.4 - - - -
613A GLY* 2.9 17.0 + - - -
614A LEU 3.6 16.2 - - - +
615A ARG* 3.2 14.4 + - - +
636A GLU* 6.1 0.7 - - - +
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Residues in contact with ALA 611 (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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566A PRO* 6.1 2.0 - - - -
607A ALA 3.0 15.8 + - - +
608A GLU* 3.0 16.1 + - - +
610A ILE* 1.3 78.5 - - - +
612A GLN* 1.3 59.9 + - + +
613A GLY 3.2 0.8 + - - -
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Residues in contact with GLN 612 (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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608A GLU* 3.0 21.1 + - + +
609A HIS* 3.4 4.7 - - - +
610A ILE 3.0 0.4 - - - -
611A ALA* 1.3 79.7 - - + +
613A GLY* 1.3 60.6 + - - +
614A LEU* 3.3 32.5 + - + +
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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