Contacts of the helix formed by residues 662 - 675 (chain B) in PDB entry 3K5N
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 TYR 662 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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652B LEU* 4.1 20.9 - - + -
655B ARG* 3.7 26.0 - - + +
656B ILE* 4.2 12.3 - - + -
660B GLU 4.1 8.3 - - - -
661B PRO* 1.3 78.4 - - + +
663B GLN* 1.3 97.5 + - + +
664B GLU 3.4 2.2 - - - -
665B TYR* 3.0 14.4 + - + +
666B VAL* 3.0 23.0 + - + +
765B LEU* 4.3 18.1 - - + +
768B ILE* 3.7 32.1 - - + +
769B GLU 5.7 2.3 - - - -
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Residues in contact with GLN 663 (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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661B PRO* 3.8 2.0 - - + +
662B TYR* 1.3 113.4 + - + +
664B GLU* 1.3 69.2 + - + +
666B VAL* 3.3 11.9 + - - +
667B ARG* 3.6 10.9 + - - +
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Residues in contact with GLU 664 (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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662B TYR 3.4 0.4 - - - -
663B GLN* 1.3 85.8 - - + +
665B TYR* 1.3 52.0 + - - +
667B ARG* 3.3 35.1 + - - +
668B GLU* 2.4 49.9 + - - +
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Residues in contact with TYR 665 (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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648B PHE* 3.9 29.8 - + - -
651B GLU* 2.3 55.2 + - + +
652B LEU* 4.3 15.5 - - + -
655B ARG* 3.8 41.3 - - - +
662B TYR 3.0 12.3 + - - +
664B GLU* 1.3 75.0 - - - +
666B VAL* 1.3 74.1 + - - +
668B GLU* 3.8 19.3 - - + +
669B THR* 3.0 34.3 + - - +
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Residues in contact with VAL 666 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
648B PHE* 4.1 30.9 - - + -
652B LEU* 4.8 7.9 - - + -
662B TYR* 3.0 30.0 + - + +
663B GLN* 3.7 6.7 - - - +
664B GLU 3.3 0.6 - - - -
665B TYR* 1.3 81.4 - - + +
667B ARG* 1.3 66.0 + - + +
669B THR* 3.0 4.9 + - - +
670B ILE* 3.0 39.8 + - + +
758B GLN* 5.0 7.0 - - - +
761B ALA* 5.9 0.2 - - + -
765B LEU* 4.7 15.0 - - + -
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Residues in contact with ARG 667 (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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663B GLN 3.6 4.3 + - - +
664B GLU* 3.3 38.2 + - - +
666B VAL* 1.3 80.9 - - + +
668B GLU* 1.3 76.6 + - - +
670B ILE* 4.0 9.2 - - + +
671B ASP* 2.8 52.6 + - - +
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Residues in contact with GLU 668 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
664B GLU* 2.4 36.1 + - - +
665B TYR* 3.5 21.3 - - + +
667B ARG* 1.3 75.9 - - - +
669B THR* 1.3 54.5 + - - +
671B ASP* 3.6 3.6 + - - +
672B LYS* 2.4 49.2 + - + +
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Residues in contact with THR 669 (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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644B LEU* 4.9 2.9 - - + -
648B PHE* 4.5 12.3 - - + -
665B TYR* 3.0 29.4 + - - +
666B VAL* 3.0 10.4 + - - +
667B ARG 3.0 0.8 - - - -
668B GLU* 1.3 79.5 - - - +
670B ILE* 1.3 62.8 + - - +
672B LYS* 2.5 33.9 + - - +
673B LEU* 2.8 7.1 + - - +
678B LEU* 3.8 17.7 - - + +
757B LEU* 4.1 20.4 - - + -
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Residues in contact with ILE 670 (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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648B PHE* 5.8 1.6 - - + -
666B VAL* 3.0 32.9 + - + +
667B ARG* 3.1 7.8 + - + +
669B THR* 1.3 70.6 - - - +
671B ASP* 1.3 68.6 + - - +
672B LYS 2.8 5.4 - - - -
673B LEU* 4.0 13.7 - - + -
674B MET* 2.8 29.7 + - + +
753B LEU* 4.6 30.3 - - + -
757B LEU* 3.9 23.8 - - + -
758B GLN* 4.6 11.7 - - + +
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Residues in contact with ASP 671 (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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667B ARG* 2.8 56.2 + - - +
668B GLU* 3.9 4.0 - - - +
670B ILE* 1.3 81.1 - - - +
672B LYS* 1.3 58.9 + - - +
674B MET* 4.6 4.6 - - - +
675B ALA* 2.9 30.0 + - - +
677B GLU* 5.1 0.2 - - - +
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Residues in contact with LYS 672 (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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668B GLU* 2.4 43.7 + - + +
669B THR* 2.5 25.2 + - - +
671B ASP* 1.3 81.0 - - + +
673B LEU* 1.3 50.1 + - - +
675B ALA* 3.5 0.7 + - - +
676B GLY 3.3 2.4 + - - -
677B GLU* 2.4 62.4 + - + +
678B LEU* 3.6 27.3 - - + +
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Residues in contact with LEU 673 (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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644B LEU* 4.2 18.4 - - + -
669B THR 2.8 10.5 + - - +
670B ILE* 3.0 26.7 + - + +
672B LYS* 1.3 68.6 - - - +
674B MET* 1.3 100.2 + - + +
675B ALA 2.9 1.8 - - - -
676B GLY* 2.3 30.0 + - - +
677B GLU 3.9 3.6 - - - +
678B LEU* 3.8 26.0 - - + +
682B LEU* 4.9 3.4 - - + -
749B TYR* 3.5 36.1 - - + -
752B TYR* 4.2 16.4 - - + -
753B LEU* 4.3 12.3 - - + +
757B LEU* 4.6 6.7 - - + -
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Residues in contact with MET 674 (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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670B ILE* 2.8 21.4 + - + +
671B ASP* 4.4 4.5 - - - +
673B LEU* 1.3 94.2 - - + +
675B ALA* 1.3 61.2 + - - +
676B GLY 3.1 0.7 + - - -
749B TYR* 3.9 43.8 - - + +
750B GLU* 4.8 10.3 - - + +
753B LEU* 5.3 10.1 - - - -
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Residues in contact with ALA 675 (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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671B ASP 2.9 23.0 + - - +
672B LYS 3.5 5.6 - - - +
673B LEU 2.9 0.4 - - - -
674B MET* 1.3 76.6 - - - +
676B GLY* 1.3 56.7 + - - +
677B GLU* 3.3 21.8 + - - +
749B TYR* 5.5 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