Contacts of the helix formed by residues 602 - 613 (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 602 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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441A GLU* 5.6 7.0 - - + +
562B ARG* 3.9 3.4 - - - +
601B PHE* 1.3 75.9 - - - +
603B ASN* 1.3 56.8 + - - +
604B SER* 3.7 5.8 + - - -
605B GLU* 3.0 31.9 + - - +
606B THR* 2.6 33.2 + - - -
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Residues in contact with ASN 603 (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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436A SER 5.6 0.4 - - - +
441A GLU* 5.9 1.0 + - - -
558B LYS* 6.4 0.2 - - - +
559B PHE 4.5 3.6 + - - -
560B PRO 4.2 1.9 + - - +
561B VAL* 3.2 37.3 - - + +
562B ARG* 2.8 32.9 + - - +
602B THR* 1.3 74.2 - - - +
604B SER* 1.3 59.4 + - - +
606B THR* 3.4 1.7 + - - -
607B ALA* 3.0 29.3 + - - +
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Residues in contact with SER 604 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
602B THR* 3.3 5.9 + - - -
603B ASN* 1.3 78.0 - - - +
605B GLU* 1.3 60.9 + - - +
607B ALA* 3.6 7.0 + - - +
608B GLU* 3.3 21.8 + - - +
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Residues in contact with GLU 605 (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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600B ARG 4.0 4.7 - - - +
601B PHE* 3.5 30.6 - - + -
602B THR* 3.0 27.9 + - - +
604B SER* 1.3 77.3 - - - +
606B THR* 1.3 62.8 + - - +
608B GLU* 3.4 6.3 + - - +
609B HIS* 2.8 55.5 + - + +
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Residues in contact with THR 606 (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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561B VAL* 4.3 10.3 - - + -
562B ARG* 2.8 24.2 + - + +
598B TYR* 3.4 40.1 - - + +
601B PHE* 3.1 22.9 - - - +
602B THR 2.6 27.1 + - - -
603B ASN 3.7 2.7 - - - -
605B GLU* 1.3 72.8 - - - +
607B ALA* 1.3 63.9 + - - +
609B HIS* 3.4 3.8 + - - +
610B ILE* 3.1 36.0 + - + +
614B LEU* 5.8 0.7 - - - -
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Residues in contact with ALA 607 (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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561B VAL* 4.4 10.5 - - + +
569B LEU* 4.6 30.6 - - + +
603B ASN 3.0 17.5 + - - +
604B SER* 3.7 8.7 - - - +
606B THR* 1.3 78.1 - - - +
608B GLU* 1.3 63.2 - - - +
610B ILE* 3.8 2.8 + - - +
611B ALA* 3.8 16.5 + - - +
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Residues in contact with GLU 608 (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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604B SER 3.3 14.0 + - - +
605B GLU* 3.4 6.9 + - - +
606B THR 3.3 0.2 - - - -
607B ALA* 1.3 79.7 - - - +
609B HIS* 1.3 81.3 + - - +
611B ALA* 3.5 7.1 + - - +
612B GLN* 3.2 56.6 + - + +
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Residues in contact with HIS 609 (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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601B PHE* 3.3 25.3 - + + -
605B GLU* 2.8 52.2 + - + +
606B THR 3.9 3.4 - - - +
608B GLU* 1.3 93.7 + - - +
610B ILE* 1.3 63.4 + - - +
612B GLN* 3.2 8.1 + - + +
613B GLY 3.1 6.2 + - - -
614B LEU* 2.8 47.5 + - + +
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Residues in contact with ILE 610 (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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561B VAL 5.7 1.3 - - - +
562B ARG 6.0 0.2 - - - +
564B SER 5.5 0.7 - - - +
566B PRO* 3.5 17.3 - - + -
569B LEU* 4.5 14.8 - - + -
581B TRP* 3.4 31.2 - - + -
598B TYR* 3.3 38.6 - - + +
606B THR* 3.1 24.2 + - + +
607B ALA 4.3 4.3 - - - +
608B GLU 3.5 0.2 - - - -
609B HIS* 1.3 73.9 - - - +
611B ALA* 1.3 63.7 + - - +
613B GLY 3.2 5.2 + - - -
614B LEU* 3.3 26.5 - - + +
615B ARG* 3.1 23.4 + - - +
636B GLU* 3.2 4.3 - - - +
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Residues in contact with ALA 611 (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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566B PRO* 4.6 8.4 - - + +
570B MET* 4.9 15.7 - - + -
607B ALA 3.8 9.8 + - - +
608B GLU* 3.5 10.7 + - - +
609B HIS 3.2 0.4 - - - -
610B ILE* 1.3 80.1 - - - +
612B GLN* 1.3 67.9 + - + +
613B GLY* 3.3 1.0 + - - -
636B GLU* 3.6 26.0 - - - +
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Residues in contact with GLN 612 (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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608B GLU* 3.2 40.5 + - - +
609B HIS* 3.2 11.5 + - + +
611B ALA* 1.3 79.9 - - - +
613B GLY* 1.3 57.5 + - - +
614B LEU 3.8 0.4 - - - +
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Residues in contact with GLY 613 (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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609B HIS 3.1 0.8 + - - -
610B ILE 3.2 8.2 + - - -
611B ALA 3.2 1.9 - - - -
612B GLN* 1.3 80.2 - - - +
614B LEU* 1.3 67.0 + - - +
615B ARG* 3.5 24.3 + - - +
631B TYR* 5.2 0.5 + - - -
636B GLU* 5.4 0.2 - - - -
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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