Contacts of the helix formed by residues 641 - 649 (chain A) in PDB entry 4L6V
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 641 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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455A TYR* 4.0 9.2 - - - -
458A ASN* 4.0 11.7 - - + -
459A ASP* 3.2 22.5 + - - +
462A ARG* 3.2 40.9 + - - +
470A MET* 4.2 3.8 - - + -
638A SER 3.5 2.5 + - - +
639A ALA 3.5 0.6 - - - -
640A ILE* 1.3 92.7 - - + +
642A ILE* 1.3 63.2 + - - +
643A ASN* 3.5 4.5 + - - +
644A GLY* 2.9 24.4 + - - -
645A TRP* 3.2 17.5 + - - -
647A ARG* 5.1 0.2 + - - -
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Residues in contact with ILE 642 (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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452A PHE* 4.3 16.4 - - + -
455A TYR* 3.7 33.9 - - + -
456A ILE* 4.6 14.6 - - + -
459A ASP* 2.4 26.8 + - - +
641A THR* 1.3 70.2 - - - +
643A ASN* 1.3 53.1 + - - +
645A TRP* 3.0 13.1 + - + +
646A LEU* 2.7 36.7 + - + +
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Residues in contact with ASN 643 (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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459A ASP* 3.3 18.4 + - - +
641A THR* 4.0 2.2 - - - +
642A ILE* 1.3 78.4 - - - +
644A GLY* 1.3 57.1 + - - +
646A LEU* 3.6 24.3 - - - +
647A ARG* 2.9 60.3 + - - +
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Residues in contact with GLY 644 (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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462A ARG* 5.0 0.2 - - - -
611A TRP* 3.8 3.0 - - - -
638A SER 3.4 22.7 - - - -
641A THR* 2.9 13.5 + - - -
642A ILE 3.1 0.2 - - - -
643A ASN* 1.3 74.9 - - - +
645A TRP* 1.3 57.6 + - - +
647A ARG* 3.7 19.0 - - - +
648A ASP* 2.7 38.2 + - - +
649A PHE 3.7 0.9 + - - -
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Residues in contact with TRP 645 (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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455A TYR* 4.1 10.1 - + - -
534A VAL* 3.9 22.9 - - + -
604A ILE* 5.2 5.6 - - + -
607A PHE* 3.5 47.8 - + + -
608A HIS* 4.0 10.5 - - + -
611A TRP* 3.4 38.4 - + - -
635A PHE* 4.4 4.9 - + - -
639A ALA* 3.3 27.6 + - + +
641A THR 3.2 25.5 + - - -
642A ILE* 3.0 16.4 + - + +
644A GLY* 1.3 72.8 - - - +
646A LEU* 1.3 65.0 + - - +
647A ARG 3.3 0.3 + - - -
649A PHE* 3.3 22.3 + + - +
650A LEU* 3.0 28.7 + - + +
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Residues in contact with LEU 646 (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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642A ILE* 2.7 24.3 + - + +
643A ASN* 3.6 26.7 - - - +
645A TRP* 1.3 73.0 - - - +
647A ARG* 1.3 58.3 + - + +
650A LEU* 3.5 20.1 - - + +
651A TRP* 3.0 26.9 + - + +
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Residues in contact with ARG 647 (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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462A ARG* 4.2 16.8 - - - +
638A SER* 4.7 1.4 + - - -
641A THR* 5.1 0.2 + - - -
643A ASN* 2.9 57.2 + - - +
644A GLY* 3.7 11.7 - - - +
646A LEU* 1.3 78.1 - - + +
648A ASP* 1.3 93.8 + - - +
649A PHE 3.3 1.6 - - - -
651A TRP* 3.4 21.8 - - + +
652A ALA* 3.0 29.5 + - - +
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Residues in contact with ASP 648 (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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611A TRP* 3.8 19.4 + - + -
631A THR* 4.4 3.1 - - - +
634A ASN* 3.6 24.2 + - - +
638A SER* 3.1 21.0 + - - -
644A GLY 2.7 15.1 + - - +
647A ARG* 1.3 116.3 + - - +
649A PHE* 1.3 58.9 + - - +
652A ALA* 3.8 15.4 - - - +
653A GLN* 4.3 5.2 + - - -
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Residues in contact with PHE 649 (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 PHE* 3.7 38.4 - + + -
610A SER* 3.6 26.7 - - - -
611A TRP* 3.5 39.3 - + + -
644A GLY 3.7 0.4 + - - -
645A TRP* 3.3 27.1 + + - +
647A ARG 3.3 0.2 - - - -
648A ASP* 1.3 81.3 - - - +
650A LEU* 1.3 82.0 + - + +
653A GLN* 3.1 65.9 + - - +
742A PHE* 4.0 15.9 - + - -
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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