Contacts of the helix formed by residues 683 - 689 (chain A) in PDB entry 4FYT
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 683 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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662A ILE* 4.4 8.3 - - + -
666A PHE* 3.5 37.7 - - + -
679A ALA 3.9 0.9 - - - +
680A LEU* 2.7 19.6 + - + +
682A ASN* 1.3 77.2 - - - +
684A LEU* 1.3 64.4 + - - +
685A PHE 3.2 3.4 - - - -
686A LEU* 3.1 35.8 + - + +
698A ALA* 4.6 4.3 - - + -
702A LEU* 4.7 6.5 - - + -
721A TYR* 2.6 32.6 + - - -
725A GLN* 3.0 13.0 + - - -
961A TRP* 4.2 0.5 - - - -
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Residues in contact with LEU 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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647A GLN* 4.2 15.9 + - - +
681A ASN* 3.2 42.1 + - + +
682A ASN 3.4 0.2 - - - -
683A THR* 1.3 78.2 + - - +
685A PHE* 1.3 60.5 + - - +
687A ILE* 3.5 13.2 - - - +
721A TYR* 3.6 20.6 - - + +
724A LYS* 6.1 2.0 - - - +
725A GLN* 3.0 20.9 + - - +
961A TRP* 3.8 14.8 - - + -
965A ASN* 3.9 18.6 - - + +
1E NAG 5.4 4.3 - - - +
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Residues in contact with PHE 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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646A LEU* 3.8 49.1 - - + +
647A GLN* 3.9 14.0 - - - +
650A HIS* 3.8 19.7 - + + -
658A ARG* 4.0 21.3 - - + -
661A ILE* 6.0 0.4 - - + -
662A ILE* 3.8 19.5 - - + -
681A ASN 4.8 0.4 + - - -
682A ASN 3.2 27.8 - - - -
683A THR 3.2 1.0 - - - -
684A LEU* 1.3 73.7 - - - +
686A LEU* 1.3 78.0 + - + +
687A ILE* 3.0 7.9 - - - -
688A GLU* 3.0 28.6 + - + +
689A GLU* 3.2 34.5 + - + -
694A PRO* 4.4 0.7 - - + -
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Residues in contact with LEU 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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662A ILE* 4.0 10.5 - - + -
683A THR* 3.1 34.4 + - + +
685A PHE* 1.3 102.1 - - + +
687A ILE* 1.3 62.4 + - - +
688A GLU 3.0 0.4 - - - -
689A GLU* 3.0 31.2 + - + +
694A PRO 4.2 11.9 - - - -
695A TRP* 3.2 46.9 + - + +
698A ALA* 3.4 30.5 - - + -
725A GLN* 4.3 3.6 - - + +
729A LEU* 5.7 0.3 - - - +
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Residues in contact with ILE 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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684A LEU 3.5 15.9 + - - +
685A PHE* 3.0 3.3 + - - +
686A LEU* 1.3 77.9 - - - +
688A GLU* 1.3 66.6 + - + +
689A GLU 5.2 0.2 - - - -
724A LYS* 3.4 35.0 - - + +
725A GLN* 3.4 36.4 - - - +
728A PRO* 3.8 35.2 - - + +
729A LEU* 4.9 4.6 + - - +
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Residues in contact with GLU 688 (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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646A LEU 4.6 4.7 - - - +
647A GLN* 4.3 19.6 + - - +
650A HIS* 3.3 40.5 + - + +
685A PHE* 3.2 16.7 - - - +
687A ILE* 1.3 85.2 - - + +
689A GLU* 1.3 61.3 + - - +
690A ARG* 3.7 9.2 + - - +
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Residues in contact with GLU 689 (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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650A HIS* 3.6 9.6 + - - -
658A ARG* 2.7 46.8 + - - -
685A PHE* 3.2 17.0 + - + -
686A LEU* 3.0 32.4 + - + +
687A ILE 5.2 0.3 - - - -
688A GLU* 1.3 77.5 - - - +
690A ARG* 1.3 63.7 + - - +
691A GLN* 2.9 28.8 + - - +
694A PRO* 3.4 12.5 - - + +
695A TRP* 3.0 36.7 + - + +
729A LEU* 3.9 9.7 - - - +
1023A SO4 4.8 0.7 + - - -
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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