Contacts of the helix formed by residues 623 - 633 (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 SER 623 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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495B THR* 5.6 4.7 - - - +
618B ARG* 3.0 12.2 + - - +
621B LEU 4.0 1.0 + - - -
622B ALA* 1.3 72.7 - - - +
624B GLU* 1.3 66.3 + - - +
625B LYS* 3.7 8.2 + - - +
626B VAL* 3.0 28.7 + - - +
627B TYR 3.0 18.9 + - - -
654B VAL* 4.5 3.6 - - - +
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Residues in contact with GLU 624 (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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618B ARG* 3.1 22.2 - - - +
623B SER* 1.3 73.5 - - - +
625B LYS* 1.3 62.8 + - - +
627B TYR* 3.4 4.8 + - - +
628B THR* 2.9 29.2 + - - +
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Residues in contact with LYS 625 (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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623B SER* 3.1 5.2 + - - +
624B GLU* 1.3 80.4 - - - +
626B VAL* 1.3 65.7 + - - +
628B THR* 3.0 21.2 + - - +
629B ILE* 3.1 17.9 + - + +
650B ASN 6.0 0.2 - - - +
653B ASP 4.8 4.7 - - - +
654B VAL* 3.6 41.0 + - + +
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Residues in contact with VAL 626 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
495B THR* 5.1 5.6 - - + -
499B LEU* 4.8 10.8 - - + -
587B MET* 5.1 5.8 - - - +
591B TYR* 3.5 50.3 - - + +
622B ALA* 3.9 7.4 - - + -
623B SER* 3.0 30.7 + - - +
625B LYS* 1.3 75.4 - - - +
627B TYR* 1.3 61.8 + - - +
629B ILE* 3.3 12.6 + - + +
630B MET* 3.2 26.5 + - + +
654B VAL* 4.2 13.5 - - + -
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Residues in contact with TYR 627 (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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615B ARG* 5.0 0.9 - - - +
616B LEU 2.7 30.3 + - - -
617B TYR* 3.9 4.1 - - - -
618B ARG* 3.3 55.6 - - + -
622B ALA* 4.7 0.6 - - - +
623B SER 3.0 4.9 + - - -
624B GLU* 3.6 7.2 - - - +
625B LYS 3.2 0.2 - - - -
626B VAL* 1.3 74.4 - - - +
628B THR* 1.3 65.9 + - - +
630B MET* 3.7 18.8 - - + -
631B TYR* 3.0 52.9 + + + +
634B TRP* 4.0 14.1 - + - -
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Residues in contact with THR 628 (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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624B GLU* 2.9 20.7 + - - +
625B LYS* 3.2 15.2 + - + +
627B TYR* 1.3 76.6 - - - +
629B ILE* 1.3 66.9 + - + +
631B TYR* 3.2 6.3 + - - +
632B SER* 3.0 24.4 + - - -
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Residues in contact with ILE 629 (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* 5.7 1.3 - - + -
587B MET* 3.6 25.1 - - + -
625B LYS* 3.1 17.2 + - + +
626B VAL* 3.5 13.9 - - + +
627B TYR 3.2 0.2 - - - -
628B THR* 1.3 77.6 - - + +
630B MET* 1.3 63.0 + - - +
632B SER* 2.6 27.5 + - - -
633B CYS* 3.7 5.2 + - - -
647B LEU* 4.1 17.3 - - + +
650B ASN* 4.0 27.1 - - + +
651B ILE* 4.2 16.8 - - + -
654B VAL* 3.6 31.2 - - + -
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Residues in contact with MET 630 (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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584B GLY 3.7 15.0 - - - +
587B MET* 3.3 26.5 - - + +
588B TRP* 3.9 34.1 - - - +
591B TYR* 4.3 3.8 - - + -
619B PRO* 4.0 17.5 - - + -
622B ALA* 4.4 3.1 - - + -
626B VAL* 3.2 29.4 + - + +
627B TYR* 3.4 25.8 - - + +
629B ILE* 1.3 78.1 - - - +
631B TYR* 1.3 62.5 - - - +
633B CYS* 3.2 21.0 + - - +
634B TRP* 3.3 32.7 - - + -
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Residues in contact with TYR 631 (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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613B GLY 5.2 0.2 + - - -
615B ARG* 3.4 43.1 + - + +
627B TYR* 3.0 53.7 + + + +
628B THR* 3.6 5.6 - - - +
630B MET* 1.3 74.1 - - - +
632B SER* 1.3 63.6 + - - +
633B CYS 3.1 2.5 - - - -
634B TRP* 3.3 30.2 + + + -
635B HIS* 3.3 18.2 + + - -
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Residues in contact with SER 632 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
628B THR* 3.0 11.9 + - - -
629B ILE* 2.6 23.0 + - - -
631B TYR* 1.3 77.5 - - - +
633B CYS* 1.3 60.4 + - - +
635B HIS* 3.1 37.9 + - - -
641B ARG* 3.7 1.7 - - - +
642B PRO* 3.4 33.7 - - - +
647B LEU* 3.8 5.9 - - - +
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Residues in contact with CYS 633 (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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580B ILE* 3.1 34.3 - - - +
581B TRP* 3.3 12.8 - - - +
583B PHE* 4.0 0.7 - - - -
584B GLY* 3.7 20.2 - - - -
587B MET* 3.8 11.4 - - - -
629B ILE 3.7 10.8 - - - -
630B MET 3.2 15.5 - - - +
631B TYR 3.1 0.2 - - - -
632B SER* 1.3 80.1 - - - +
634B TRP* 1.3 59.0 + - + +
635B HIS 3.5 0.4 - - - -
641B ARG* 3.0 22.7 + - - -
647B LEU* 4.0 22.7 - - - -
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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