Contacts of the helix formed by residues 756 - 765 (chain A) in PDB entry 3K5M
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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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641A TRP* 3.2 25.1 - - - +
642A THR* 2.7 49.3 + - + +
644A LEU* 4.6 6.7 - - + -
645A ALA* 3.3 18.0 - - + +
684A TYR* 3.4 32.3 + - - +
752A TYR* 2.9 27.7 + - + +
755A ARG* 1.3 92.7 - - - +
757A LEU* 1.3 65.2 + - - +
758A GLN 3.4 0.9 - - - -
759A PRO* 3.4 7.2 - - - +
760A VAL* 3.5 19.8 + - - +
811T T 5.8 1.6 - - - +
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Residues in contact with LEU 757 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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644A LEU* 3.8 34.5 - - + +
645A ALA* 5.0 0.4 - - - +
648A PHE* 3.3 48.6 - - + -
669A THR* 3.8 23.1 - - + -
670A ILE* 4.1 21.1 - - + -
673A LEU* 3.8 24.2 - - + -
752A TYR 3.0 12.3 + - - +
753A LEU* 3.7 13.0 - - + +
756A GLN* 1.3 74.4 - - - +
758A GLN* 1.3 63.7 + - - +
760A VAL* 3.3 2.9 + - - +
761A ALA* 3.2 17.5 + - - +
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Residues in contact with GLN 758 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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607A ARG* 4.7 4.5 - - - +
753A LEU* 3.0 22.0 + - + +
754A THR* 3.7 11.7 - - - +
757A LEU* 1.3 73.4 - - - +
759A PRO* 1.3 74.5 - - + +
761A ALA* 3.1 8.3 + - - +
762A GLU* 3.0 24.4 + - - +
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Residues in contact with PRO 759 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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607A ARG* 3.6 31.0 + - - +
635A GLU* 5.1 7.1 - - - +
641A TRP* 4.2 11.0 - - + -
754A THR 3.4 11.4 - - - +
755A ARG* 3.5 20.0 - - - +
756A GLN 3.4 13.0 - - - +
758A GLN* 1.3 96.6 - - + +
760A VAL* 1.3 59.5 + - - +
762A GLU* 3.6 3.4 + - + +
763A GLY* 3.3 16.8 + - - -
811T T 3.5 22.4 - - - +
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Residues in contact with VAL 760 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
635A GLU* 4.7 7.9 - - + -
641A TRP* 4.7 7.6 - - + -
645A ALA* 4.0 23.6 - - + +
648A PHE* 3.6 20.6 - - + -
649A GLN* 3.6 44.6 + - + +
652A LEU* 4.3 5.8 - - + -
653A TYR* 4.4 5.4 + - + -
756A GLN 3.5 14.8 - - - +
757A LEU 3.3 8.9 + - - +
758A GLN 3.1 0.6 - - - -
759A PRO* 1.3 78.6 - - - +
761A ALA* 1.3 62.3 + - - +
763A GLY* 3.2 13.1 + - - -
764A ILE* 3.8 7.6 + - - +
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Residues in contact with ALA 761 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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648A PHE* 4.6 9.4 - - + -
652A LEU* 4.0 12.6 - - + -
666A VAL* 6.0 3.1 - - + -
757A LEU 3.2 8.6 + - - +
758A GLN* 3.1 12.0 + - - +
760A VAL* 1.3 75.8 - - - +
762A GLU* 1.3 60.5 + - - +
764A ILE* 3.1 1.9 + - - +
765A LEU* 2.8 54.2 + - + +
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Residues in contact with GLU 762 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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605A THR* 5.6 2.3 + - - -
607A ARG* 4.7 16.2 - - + +
758A GLN 3.0 15.5 + - - +
759A PRO* 3.6 9.6 - - + +
761A ALA* 1.3 76.8 - - - +
763A GLY* 1.3 61.8 + - - +
766A PRO* 3.2 25.6 - - + +
767A PHE* 5.9 0.3 - - - -
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Residues in contact with GLY 763 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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602A LEU* 4.6 2.6 - - - +
604A PRO* 4.5 12.7 - - - +
605A THR* 5.4 1.2 + - - -
649A GLN* 6.3 0.2 - - - -
653A TYR* 4.2 11.8 + - - -
759A PRO 3.3 7.6 + - - -
760A VAL 3.2 9.2 + - - -
761A ALA 3.0 1.4 - - - -
762A GLU* 1.3 81.5 - - - +
764A ILE* 1.3 59.1 + - - +
766A PRO* 4.7 0.2 - - - -
767A PHE* 3.8 18.5 - - - -
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Residues in contact with ILE 764 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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411A LEU* 5.6 2.4 - - + +
602A LEU* 3.4 24.5 - - + -
652A LEU* 3.9 22.4 - - + -
653A TYR* 3.3 52.5 - - + +
656A ILE* 3.5 38.1 - - + -
657A PHE* 5.3 3.6 - - + -
760A VAL 3.8 1.5 + - - +
761A ALA 3.1 5.8 + - - +
763A GLY* 1.3 79.5 - - - +
765A LEU* 1.3 72.2 + - + +
766A PRO* 3.3 3.1 - - - -
767A PHE* 3.2 22.5 + - - +
768A ILE* 3.8 4.3 - - - +
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Residues in contact with LEU 765 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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652A LEU* 4.5 8.3 - - + -
656A ILE* 3.4 16.2 - - + -
662A TYR* 3.8 21.8 - - + +
666A VAL* 5.0 9.0 - - + -
761A ALA* 2.8 41.1 + - + +
764A ILE* 1.3 79.1 - - + +
766A PRO* 1.3 65.2 - - + +
768A ILE* 2.9 44.3 + - + +
770A ASP* 3.1 40.2 + - + +
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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