Contacts of the helix formed by residues 672 - 687 (chain A) in PDB entry 5L6P
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 672 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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670A GLY 5.3 2.0 - - - +
671A TYR* 1.3 85.2 - - - +
673A GLU* 1.4 63.7 + - - +
674A ARG* 3.9 6.3 + - - +
675A GLN* 2.8 41.6 + - - +
676A ARG* 3.2 17.5 + - - +
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Residues in contact with GLU 673 (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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671A TYR* 6.2 0.2 - - - -
672A THR* 1.4 73.6 - - - +
674A ARG* 1.3 61.6 + - - +
676A ARG* 3.7 5.4 + - - +
677A ARG* 3.4 37.8 + - - +
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Residues in contact with ARG 674 (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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672A THR* 3.3 6.8 + - - +
673A GLU* 1.3 76.5 - - - +
675A GLN* 1.4 53.6 + - + +
677A ARG* 3.3 10.4 + - - +
678A ASP* 2.9 48.1 + - - +
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Residues in contact with GLN 675 (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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643A GLU 5.8 1.4 + - - -
644A PHE* 3.7 27.8 - - + -
667A LEU* 4.1 4.2 - - + +
670A GLY 4.5 1.9 - - - +
671A TYR* 3.5 15.8 - - + -
672A THR* 2.8 43.8 + - - +
674A ARG* 1.4 79.3 - - + +
676A ARG* 1.4 55.1 + - - +
678A ASP* 4.5 1.3 - - - +
679A PHE* 3.0 31.0 + - - +
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Residues in contact with ARG 676 (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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667A LEU* 3.9 17.9 - - + -
671A TYR* 3.7 33.7 + - + -
672A THR 3.2 14.5 + - - +
673A GLU* 4.0 6.1 - - - +
674A ARG 3.4 0.2 - - - -
675A GLN* 1.4 74.0 - - - +
677A ARG* 1.4 64.4 + - + +
679A PHE* 3.8 1.6 + - - +
680A LEU* 3.2 57.1 + - + +
702A THR* 4.1 24.0 + - - +
707A VAL* 4.2 16.5 - - + +
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Residues in contact with ARG 677 (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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673A GLU* 3.4 23.3 + - - +
674A ARG* 3.3 12.2 + - - +
676A ARG* 1.4 77.8 - - + +
678A ASP* 1.4 59.7 + - - +
680A LEU* 3.6 4.3 + - - +
681A SER* 2.9 31.8 + - - -
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Residues in contact with ASP 678 (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 PHE* 3.6 25.6 - - + -
674A ARG* 2.9 31.3 + - - +
675A GLN* 4.4 1.4 + - - +
676A ARG 3.4 0.2 - - - -
677A ARG* 1.4 76.3 - - - +
679A PHE* 1.3 63.1 + - - +
681A SER* 3.1 20.4 + - - -
682A GLU* 3.4 17.7 + - - +
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Residues in contact with PHE 679 (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 PHE* 3.6 36.9 - + + -
665A LYS* 3.7 44.0 - - + -
666A THR 4.4 7.0 - - - -
667A LEU* 3.8 24.9 - - + -
675A GLN 3.0 20.1 + - - +
676A ARG 4.0 2.5 - - - +
677A ARG 3.5 0.2 - - - -
678A ASP* 1.3 76.0 - - - +
680A LEU* 1.4 66.6 + - + +
682A GLU* 3.5 12.0 + - - +
707A VAL* 3.7 38.1 - - + -
708A MET 4.6 0.4 - - - -
709A ILE* 3.4 46.7 - - + +
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Residues in contact with LEU 680 (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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676A ARG* 3.2 55.3 + - + +
677A ARG* 4.1 3.6 - - - +
679A PHE* 1.4 92.6 - - + +
681A SER* 1.4 62.6 + - - +
682A GLU 3.2 0.4 - - - -
683A ALA* 3.1 17.9 + - + +
684A SER* 3.2 15.1 + - - -
700A VAL* 3.8 29.2 - - + -
702A THR* 4.2 14.8 - - + -
707A VAL* 4.6 9.6 - - + -
709A ILE* 5.1 0.7 - - + -
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Residues in contact with SER 681 (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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677A ARG 2.9 17.1 + - - -
678A ASP* 3.1 20.8 + - - -
679A PHE 3.5 0.2 - - - -
680A LEU* 1.4 74.0 - - - +
682A GLU* 1.4 58.3 + - - +
684A SER* 3.2 12.7 + - - -
685A ILE* 3.2 37.1 + - - +
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Residues in contact with GLU 682 (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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643A GLU* 4.0 11.2 - - - +
644A PHE* 3.4 35.2 - - - -
665A LYS* 3.6 13.6 + - - +
678A ASP* 3.4 9.4 + - - +
679A PHE 3.5 8.8 - - - +
680A LEU 3.2 0.6 - - - -
681A SER* 1.4 77.6 + - - +
683A ALA* 1.3 60.5 + - - +
685A ILE* 3.7 12.5 + - + +
686A MET* 3.4 29.5 + - - +
709A ILE* 5.3 0.7 - - - -
777A PHE* 3.3 52.9 - - + +
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Residues in contact with ALA 683 (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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679A PHE 3.7 1.0 + - - -
680A LEU* 3.1 15.0 + - + +
682A GLU* 1.3 77.9 - - - +
684A SER* 1.4 53.9 + - - +
686A MET* 3.5 5.3 + - - +
687A GLY* 2.8 32.1 + - - -
697A LEU* 3.7 12.5 - - + +
700A VAL* 3.8 29.8 - - + -
709A ILE* 3.8 24.7 - - + +
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Residues in contact with SER 684 (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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680A LEU 3.2 11.7 + - - -
681A SER* 3.2 15.0 + - - -
683A ALA* 1.4 73.2 - - - +
685A ILE* 1.4 62.9 + - - +
687A GLY* 3.6 2.7 + - - -
688A GLN* 3.3 35.1 + - - +
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Residues in contact with ILE 685 (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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681A SER* 3.2 26.1 + - - +
682A GLU* 3.9 13.2 - - + +
683A ALA 3.4 0.4 - - - -
684A SER* 1.4 74.9 - - - +
686A MET* 1.3 62.0 + - - +
688A GLN* 3.3 21.4 + - - +
689A PHE* 3.0 28.3 - - + -
754A TYR* 3.6 39.7 - - + +
777A PHE* 4.2 19.3 - - + -
1002A DIO 4.2 0.7 - - - -
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Residues in contact with MET 686 (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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665A LYS* 5.6 1.6 - - - -
682A GLU 3.4 19.8 + - - +
683A ALA* 3.8 5.4 - - - +
685A ILE* 1.3 75.2 - - - +
687A GLY* 1.3 60.6 + - - +
688A GLN 3.2 1.7 + - - -
689A PHE* 3.3 22.3 + - - +
695A ILE* 3.7 38.2 - - + +
697A LEU* 4.5 15.3 + - + +
709A ILE* 5.1 7.2 - - - -
711A THR* 3.6 29.2 - - + -
776A ASP 4.2 7.4 - - - +
777A PHE* 4.2 6.7 - - + -
1001A 6P8 3.9 25.4 - - + -
1002A DIO 3.4 29.4 - - - +
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Residues in contact with GLY 687 (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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683A ALA 2.8 21.7 + - - -
684A SER* 4.0 5.2 - - - -
685A ILE 3.3 0.6 - - - -
686A MET* 1.3 71.5 - - - +
688A GLN* 1.3 58.9 + - - +
689A PHE 3.4 3.1 + - - +
697A LEU* 3.8 20.0 - - - -
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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