Contacts of the helix formed by residues 756 - 765 (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 GLN 756 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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641B TRP* 2.5 39.2 - - - -
642B THR* 1.9 64.6 + - - +
644B LEU* 4.3 2.9 - - + -
645B ALA* 3.6 7.8 - - + +
684B TYR* 3.6 26.3 + - + +
752B TYR* 2.6 25.6 + - + +
755B ARG* 1.3 74.4 - - + +
757B LEU* 1.3 70.4 + - + +
759B PRO* 3.1 15.2 - - - +
760B VAL* 3.7 20.1 + - - +
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Residues in contact with LEU 757 (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* 2.7 51.6 - - + -
645B ALA* 4.8 0.4 - - - +
648B PHE* 3.3 44.1 - - + -
669B THR* 4.1 18.6 - - + -
670B ILE* 3.9 28.0 - - + -
673B LEU* 4.6 11.0 - - + -
752B TYR 4.0 2.9 - - - +
753B LEU* 3.3 16.3 + - + +
756B GLN* 1.3 75.7 - - + +
758B GLN* 1.3 61.0 + - + +
759B PRO* 3.1 7.9 - - - -
760B VAL 3.6 0.5 + - - -
761B ALA* 3.5 10.0 + - - +
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Residues in contact with GLN 758 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
648B PHE* 6.0 0.9 - - - -
666B VAL* 5.0 6.4 - - - +
670B ILE* 4.6 12.8 - - + +
753B LEU* 3.0 40.7 + - + +
754B THR* 4.3 7.4 - - - +
757B LEU* 1.3 73.1 - - + +
759B PRO* 1.3 70.5 - - + +
761B ALA* 4.5 11.9 - - - +
762B GLU* 3.7 22.7 + - - +
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Residues in contact with PRO 759 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
635B GLU* 4.6 5.4 - - - +
641B TRP* 4.5 12.3 - - + -
754B THR 3.3 22.0 - - - +
755B ARG* 3.4 17.3 - - - +
756B GLN 3.1 11.7 - - - +
757B LEU 3.1 4.3 - - - -
758B GLN* 1.3 96.7 - - - +
760B VAL* 1.3 63.7 + - - +
761B ALA 3.1 1.3 - - - -
762B GLU* 3.1 17.9 + - + +
763B GLY* 3.3 9.0 + - - -
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Residues in contact with VAL 760 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
635B GLU* 4.1 28.2 - - + +
641B TRP* 4.8 0.9 - - + -
645B ALA* 4.2 20.9 - - + +
648B PHE* 3.7 22.7 - - + -
649B GLN* 4.1 33.5 + - + -
652B LEU* 4.5 5.8 - - + -
653B TYR* 4.8 6.1 + - + -
756B GLN 3.7 13.2 - - - +
757B LEU 3.8 7.6 - - - +
759B PRO* 1.3 82.0 - - - +
761B ALA* 1.3 62.2 + - - +
763B GLY* 3.4 9.0 + - - -
764B ILE* 3.7 10.9 + - - +
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Residues in contact with ALA 761 (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* 4.3 12.3 - - + -
652B LEU* 4.5 8.3 - - + -
666B VAL* 5.9 0.9 - - + -
757B LEU 3.5 13.0 + - - +
758B GLN* 4.5 16.2 - - - +
760B VAL* 1.3 81.0 - - - +
762B GLU* 1.3 65.2 + - - +
763B GLY 3.0 2.2 - - - -
764B ILE* 4.6 1.3 - - - -
765B LEU* 2.8 49.5 + - + +
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Residues in contact with GLU 762 (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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758B GLN 3.7 15.7 + - - +
759B PRO* 3.1 15.0 + - + +
761B ALA* 1.3 78.5 - - - +
763B GLY* 1.3 56.7 + - - +
765B LEU* 5.1 0.4 - - - -
766B PRO* 2.7 40.9 - - + +
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Residues in contact with GLY 763 (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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602B LEU* 4.8 3.4 - - - +
604B PRO* 5.0 6.6 - - - +
635B GLU* 6.0 1.6 - - - -
653B TYR* 5.1 4.0 - - - -
759B PRO 3.3 8.7 + - - -
760B VAL 3.4 4.4 + - - -
761B ALA 3.0 1.0 - - - -
762B GLU* 1.3 82.2 - - - +
764B ILE* 1.3 55.0 + - - +
766B PRO* 4.8 0.3 - - - +
767B PHE* 3.4 22.2 - - - -
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Residues in contact with ILE 764 (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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411B LEU* 4.7 10.1 - - + +
602B LEU* 3.9 20.6 - - + -
652B LEU* 4.0 25.4 - - + -
653B TYR* 4.1 42.6 + - + +
656B ILE* 3.1 36.3 - - + -
657B PHE* 5.3 2.0 - - + -
760B VAL 3.7 5.5 + - - +
761B ALA 3.2 4.0 + - - +
763B GLY* 1.3 76.9 - - - +
765B LEU* 1.3 73.2 + - + +
766B PRO 3.5 1.3 - - - -
767B PHE* 3.8 16.2 + - - +
768B ILE* 4.5 6.1 - - - +
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Residues in contact with LEU 765 (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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652B LEU* 4.7 4.9 - - + -
656B ILE* 4.0 17.5 - - + -
662B TYR* 4.3 23.3 - - + +
666B VAL* 4.7 14.6 - - + -
761B ALA* 2.8 34.5 + - + +
762B GLU* 5.1 0.2 - - - -
764B ILE* 1.3 79.1 - - + +
766B PRO* 1.3 72.6 - - + +
768B ILE* 3.0 44.5 - - + +
769B GLU 3.3 9.3 + - - -
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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