Contacts of the helix formed by residues 771 - 779 (chain B) in PDB entry 3KZ1
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 PRO 771 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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768B ASN* 5.7 1.1 - - - +
770B MET* 1.4 89.8 - - + +
772B ARG* 1.3 67.5 + - - +
773B GLU* 3.2 4.0 - - + +
774B GLU* 3.0 36.8 + - + +
775B LEU* 3.0 10.7 + - - +
846B LYS* 6.1 2.0 - - - -
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Residues in contact with ARG 772 (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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761B TYR* 5.5 4.5 - - - -
765B LYS* 3.5 55.2 + - - +
768B ASN* 4.3 14.5 + - - +
770B MET 3.7 1.8 + - - -
771B PRO* 1.3 72.4 - - - +
773B GLU* 1.3 63.1 + - + +
775B LEU* 3.2 20.2 + - - +
776B ALA* 2.9 31.3 + - + +
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Residues in contact with GLU 773 (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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771B PRO* 3.2 4.4 - - + +
772B ARG* 1.3 81.3 - - + +
774B GLU* 1.3 60.2 + - - +
776B ALA* 3.5 9.3 + - - +
777B ARG* 3.2 39.9 + - - +
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Residues in contact with GLU 774 (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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770B MET* 4.0 26.3 - - + +
771B PRO* 3.0 30.1 + - + +
773B GLU* 1.3 74.4 - - - +
775B LEU* 1.3 65.4 + - - +
776B ALA 3.1 1.1 - - - -
777B ARG* 3.0 32.0 + - + +
778B LEU* 3.3 10.7 + - - +
842B LEU* 3.6 30.5 - - + +
843B ILE* 4.5 5.6 - - + +
846B LYS* 3.7 20.2 - - - +
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Residues in contact with LEU 775 (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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761B TYR* 3.9 26.1 - - + -
764B MET* 3.8 35.4 - - + +
765B LYS* 3.7 39.5 - - + +
770B MET* 3.8 19.6 - - + +
771B PRO 3.0 11.2 + - - +
772B ARG* 3.4 24.9 - - - +
774B GLU* 1.3 75.5 - - - +
776B ALA* 1.3 57.0 + - - +
778B LEU* 3.4 6.4 + - + +
779B PHE* 3.0 31.4 + - + +
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Residues in contact with ALA 776 (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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761B TYR* 5.8 1.1 - - - -
772B ARG* 2.9 20.1 + - + +
773B GLU* 3.7 10.5 - - - +
774B GLU 3.1 0.6 - - - -
775B LEU* 1.3 74.4 - - - +
777B ARG* 1.3 61.4 + - + +
779B PHE 4.0 7.4 - - - +
780B PRO* 3.0 36.6 - - + +
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Residues in contact with ARG 777 (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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773B GLU* 3.2 39.8 + - - +
774B GLU* 3.0 22.8 + - + +
776B ALA* 1.3 80.6 - - - +
778B LEU* 1.3 62.9 + - - +
780B PRO* 3.7 12.8 - - - +
832B PHE 5.5 0.7 - - - +
835B TYR* 3.6 69.4 + - + +
836B GLN* 5.1 1.6 + - - -
839B ALA* 4.3 2.4 - - + +
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Residues in contact with LEU 778 (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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764B MET* 3.7 22.9 - - + -
770B MET* 4.3 10.1 - - + -
774B GLU 3.3 10.0 + - - +
775B LEU* 3.5 13.2 - - + +
777B ARG* 1.3 79.9 - - - +
779B PHE* 1.3 88.9 + - + +
780B PRO* 3.5 5.4 - - - +
832B PHE* 4.4 5.5 - - - +
836B GLN* 5.6 4.6 - - + +
839B ALA* 4.0 20.9 - - + +
840B LEU* 5.1 7.0 - - + -
843B ILE* 4.5 20.6 - - + -
871B LEU* 4.9 7.6 - - + -
875B ILE* 3.6 30.1 - - + +
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Residues in contact with PHE 779 (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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756B LEU* 4.2 15.0 - - + -
760B PHE* 4.2 17.5 - - + -
761B TYR* 3.5 49.0 + + + -
764B MET* 4.0 12.8 - - - -
775B LEU* 3.0 12.3 + - + +
776B ALA* 3.2 8.4 - - - +
778B LEU* 1.3 111.2 - - + +
780B PRO* 1.4 68.8 - - - +
781B ASN 3.5 2.0 - - - -
782B LEU* 3.7 31.2 + - + +
832B PHE* 4.2 10.3 - + - -
871B LEU* 4.4 9.4 - - + -
875B ILE* 3.6 23.8 - - + -
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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