Contacts of the helix formed by residues 683 - 693 (chain B) in PDB entry 3T6A
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 683 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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638B LYS* 5.4 4.0 - - - +
678B ILE* 5.9 0.9 - - - +
679B LEU* 3.0 42.8 + - + +
682B LYS* 1.3 88.9 + - + +
684B LEU* 1.3 66.7 + - + +
686B PRO* 3.3 5.0 - - - +
687B PHE* 3.1 30.7 + - - +
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Residues in contact with LEU 684 (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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631B ILE* 4.1 14.8 - - + +
634B ALA* 4.7 3.1 - - + -
635B VAL* 3.8 27.1 - - + -
638B LYS* 4.0 26.9 - - + +
639B ASP* 6.1 0.2 - - - +
647B PHE* 3.9 19.3 - - + -
651B MET* 3.7 17.3 - - + +
679B LEU* 3.2 11.6 + - + +
680B TYR* 3.4 31.2 + - + +
683B GLN* 1.3 87.9 - - + +
685B LYS* 1.3 56.2 + - - +
687B PHE* 3.3 3.6 + - - +
688B SER* 2.7 37.1 + - - -
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Residues in contact with LYS 685 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
651B MET* 4.1 7.2 - - + -
655B GLU* 4.7 15.9 - - - +
680B TYR* 3.0 49.3 + - + +
681B GLU* 2.6 39.1 + - - +
684B LEU* 1.3 73.9 - - - +
686B PRO* 1.4 70.0 - - + +
688B SER* 3.0 5.6 + - - -
689B LYS* 3.0 22.1 + - - +
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Residues in contact with PRO 686 (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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681B GLU 3.5 12.1 - - - +
682B LYS* 3.3 21.1 - - - +
683B GLN 3.3 15.9 - - - +
685B LYS* 1.4 95.5 - - + +
687B PHE* 1.3 60.4 + - - +
689B LYS* 3.3 11.4 + - + +
690B LEU* 3.1 26.5 + - - +
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Residues in contact with PHE 687 (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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638B LYS* 3.7 39.5 - - + -
644B LEU* 4.1 16.2 - - + -
647B PHE* 3.6 34.3 - + - -
683B GLN 3.1 20.4 + - - +
684B LEU 3.7 2.2 - - - +
686B PRO* 1.3 74.2 - - - +
688B SER* 1.3 65.5 + - - +
690B LEU* 3.2 12.3 + - + +
691B LEU* 3.0 46.0 + - + +
699B CYS* 3.4 43.7 - - + -
701B PRO* 4.4 4.0 - - + -
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Residues in contact with SER 688 (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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647B PHE* 4.6 4.3 - - - -
648B SER* 5.7 2.3 - - - -
651B MET* 3.8 33.6 - - - +
655B GLU* 4.1 10.0 + - - -
684B LEU 2.7 21.1 + - - -
685B LYS* 3.2 6.7 - - - -
687B PHE* 1.3 80.2 - - - +
689B LYS* 1.3 57.5 + - - +
691B LEU* 3.2 10.2 + - - +
692B HIS* 3.1 26.7 + - - +
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Residues in contact with LYS 689 (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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685B LYS 3.0 11.3 + - - +
686B PRO* 3.4 13.0 - - + +
687B PHE 3.2 0.2 - - - -
688B SER* 1.3 73.6 - - - +
690B LEU* 1.3 67.1 + - + +
692B HIS* 3.2 9.1 + - + +
693B GLU* 2.8 55.0 + - - +
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Residues in contact with LEU 690 (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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686B PRO 3.1 15.8 + - - +
687B PHE* 3.2 12.8 + - + +
689B LYS* 1.3 78.9 - - + +
691B LEU* 1.3 64.0 + - - +
693B GLU* 3.3 19.9 + - - +
695B ARG* 3.1 45.1 + - + +
699B CYS* 4.2 31.9 - - + -
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Residues in contact with LEU 691 (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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644B LEU* 4.3 14.4 - - + -
647B PHE* 4.1 18.6 - - + -
648B SER* 5.2 1.3 - - - -
687B PHE* 3.0 53.0 + - + +
688B SER* 3.4 10.1 - - - +
689B LYS 3.2 0.2 - - - -
690B LEU* 1.3 76.6 - - - +
692B HIS* 1.3 58.4 + - - +
694B GLY* 2.9 20.6 + - - -
695B ARG 4.1 1.7 + - - +
696B GLU* 3.4 35.4 + - + +
699B CYS* 4.6 1.6 - - - -
709B LEU* 3.4 42.5 - - + +
743B HIS* 3.6 1.0 - - - -
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Residues in contact with HIS 692 (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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688B SER 3.1 13.1 + - - +
689B LYS* 3.2 12.1 + - + +
691B LEU* 1.3 72.7 - - - +
693B GLU* 1.3 62.8 + - + +
694B GLY 3.0 4.9 - - - -
709B LEU* 4.7 5.6 - - - -
712B PRO* 4.7 6.8 - - + +
728B ASP* 4.2 28.1 + - - -
730B TRP* 5.2 7.1 - + - -
734B ASP* 3.0 40.1 + - - -
739B ILE* 3.6 8.8 - - + +
743B HIS* 2.9 20.9 + - - -
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Residues in contact with GLU 693 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
689B LYS* 2.8 57.8 + - - +
690B LEU* 3.8 22.6 - - - +
691B LEU 3.3 0.2 - - - -
692B HIS* 1.3 78.8 - - + +
694B GLY* 1.3 58.3 + - - +
695B ARG* 3.4 16.1 + - + +
739B ILE* 3.9 32.6 - - + +
742B ASN* 3.0 27.3 + - - +
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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