Contacts of the helix formed by residues 683 - 693 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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638A LYS* 5.8 4.5 - - - +
679A LEU* 3.0 41.2 + - + +
681A GLU 3.5 0.2 - - - -
682A LYS* 1.3 88.4 + - + +
684A LEU* 1.3 65.8 + - + +
686A PRO* 3.3 5.1 - - - +
687A PHE* 3.1 30.2 + - - +
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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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631A ILE* 3.8 31.2 - - + +
634A ALA* 4.6 6.1 - - + -
635A VAL* 3.9 22.7 - - + -
638A LYS* 4.1 25.1 - - + +
639A ASP* 6.0 0.9 - - - +
647A PHE* 4.0 17.2 - - + -
651A MET* 3.6 18.8 - - + +
679A LEU* 3.1 12.3 + - + +
680A TYR* 3.4 23.1 - - + +
683A GLN* 1.3 85.3 - - + +
685A LYS* 1.3 60.2 + - - +
687A PHE* 3.8 3.5 - - - +
688A SER* 2.9 31.5 + - - -
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Residues in contact with LYS 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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651A MET* 4.1 9.0 - - + -
655A GLU* 4.8 16.2 - - - +
660A THR* 5.9 1.4 + - - -
680A TYR* 3.0 40.0 + - + +
681A GLU* 2.7 49.6 + - - +
684A LEU* 1.3 71.3 - - - +
686A PRO* 1.3 72.5 - - + +
688A SER* 3.2 5.9 + - - -
689A LYS* 3.1 21.7 + - - +
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Residues in contact with PRO 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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681A GLU 3.4 10.5 - - - +
682A LYS* 3.2 21.8 - - - +
683A GLN* 3.3 14.6 - - - +
685A LYS* 1.3 95.5 - - + +
687A PHE* 1.3 60.5 + - - +
689A LYS* 3.1 14.2 + - + +
690A LEU* 3.0 26.0 + - - +
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Residues in contact with PHE 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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638A LYS* 3.5 46.2 - - + +
644A LEU* 4.0 17.0 - - + -
647A PHE* 3.8 14.6 - + - -
683A GLN 3.1 20.1 + - - +
684A LEU* 3.8 2.7 - - - +
686A PRO* 1.3 73.2 - - - +
688A SER* 1.3 68.0 + - - +
690A LEU* 3.2 12.8 + - + +
691A LEU* 3.0 52.0 + - + +
699A CYS* 3.3 40.4 - - + -
700A VAL 5.3 0.2 - - - -
701A PRO* 4.0 10.5 - - + -
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Residues in contact with SER 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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647A PHE* 4.5 7.7 - - - -
648A SER* 5.9 1.4 - - - -
651A MET* 4.0 23.2 - - - +
655A GLU* 4.1 14.2 + - - -
684A LEU 2.9 19.7 + - - -
685A LYS* 3.2 7.2 - - - -
687A PHE* 1.3 77.7 - - - +
689A LYS* 1.3 62.2 + - - +
691A LEU* 3.3 12.7 + - - +
692A HIS* 3.1 21.8 + - - +
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Residues in contact with LYS 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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685A LYS 3.1 11.8 + - - +
686A PRO* 3.3 14.6 - - + +
687A PHE 3.1 0.2 - - - -
688A SER* 1.3 72.7 - - - +
690A LEU* 1.3 70.0 + - + +
692A HIS* 3.0 8.9 + - + +
693A GLU* 2.7 56.2 + - + +
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Residues in contact with LEU 690 (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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686A PRO 3.0 16.0 + - - +
687A PHE* 3.3 14.1 - - + +
689A LYS* 1.3 77.7 - - + +
691A LEU* 1.3 63.5 + - - +
693A GLU* 3.1 29.0 + - - +
694A GLY 3.3 0.3 + - - -
695A ARG* 3.2 39.7 + - + +
699A CYS* 3.9 32.8 - - + -
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Residues in contact with LEU 691 (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* 4.2 14.1 - - + -
647A PHE* 4.0 21.5 - - + -
648A SER* 5.5 0.2 - - - -
687A PHE* 3.0 57.9 + - + +
688A SER* 3.5 8.1 - - - +
689A LYS 3.2 0.2 - - - -
690A LEU* 1.3 75.4 - - - +
692A HIS* 1.3 58.8 + - - +
694A GLY* 2.9 21.1 + - - -
695A ARG 4.1 3.3 + - - +
696A GLU* 3.7 33.5 + - + +
699A CYS* 4.5 2.7 - - - -
709A LEU* 3.5 41.0 - - + +
743A HIS* 3.5 2.1 - - - -
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Residues in contact with HIS 692 (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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688A SER 3.1 12.7 + - - +
689A LYS* 3.0 12.4 + - + +
691A LEU* 1.3 72.9 - - - +
693A GLU* 1.3 60.0 + - + +
694A GLY 3.0 5.4 - - - -
709A LEU* 4.7 4.5 - - - -
712A PRO* 4.4 7.7 - - + +
728A ASP* 3.2 37.0 + - - -
730A TRP* 5.4 6.9 - + - -
734A ASP* 3.5 28.9 + - - +
739A ILE* 3.7 6.5 - - + +
743A HIS* 3.0 20.4 + - - -
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Residues in contact with GLU 693 (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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689A LYS* 2.7 57.1 + - + +
690A LEU* 3.1 26.8 + - - +
692A HIS* 1.3 80.4 - - + +
694A GLY* 1.3 59.1 + - - +
695A ARG* 3.5 11.1 + - + +
739A ILE* 3.7 25.4 - - + +
742A ASN* 3.2 25.9 + - - +
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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