Contacts of the helix formed by residues 662 - 673 (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 LEU 662 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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613A ILE* 4.4 13.2 - - + -
614A LEU* 4.3 13.7 - - + -
623A ARG* 4.7 6.1 - - - +
627A LEU* 6.4 0.2 - - + -
658A GLN 3.6 11.0 - - - +
659A ILE* 3.0 37.0 + - + +
660A THR 3.2 0.4 - - - -
661A ARG* 1.3 76.2 - - + +
663A GLU* 1.3 63.7 + - - +
664A LYS 3.3 2.9 - - - -
665A THR* 3.0 24.2 + - + +
666A TRP* 3.1 18.5 + - + +
812A SER* 3.6 31.6 - - - +
815A LEU* 4.9 4.5 - - + -
816A GLU* 3.3 28.0 - - + +
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Residues in contact with GLU 663 (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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660A THR 4.5 9.9 - - - +
661A ARG* 2.9 12.6 + - - +
662A LEU* 1.3 71.4 - - - +
664A LYS* 1.3 64.2 + - + +
666A TRP* 3.3 2.4 + - - +
667A THR* 2.8 34.9 + - - +
670A ARG* 3.3 35.1 + - - -
816A GLU* 3.1 4.1 + - - +
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Residues in contact with LYS 664 (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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620A LEU* 3.7 22.5 - - + +
663A GLU* 1.3 79.3 - - + +
665A THR* 1.3 57.7 + - - +
667A THR* 3.6 6.9 + - - +
668A ALA* 3.1 27.2 + - - +
816A GLU* 2.9 33.2 + - + +
817A PRO* 4.8 12.3 + - - +
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Residues in contact with THR 665 (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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613A ILE* 5.5 0.9 - - + -
620A LEU* 3.3 7.2 - - + +
623A ARG* 3.1 31.5 + - + +
624A ALA* 3.9 23.5 - - - +
627A LEU* 3.8 22.7 - - + -
662A LEU* 3.0 20.7 + - + +
664A LYS* 1.3 77.5 - - - +
666A TRP* 1.3 60.4 + - + +
668A ALA* 3.4 4.5 + - - +
669A LEU* 3.0 24.6 + - - +
816A GLU* 2.7 19.7 + - - -
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Residues in contact with TRP 666 (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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627A LEU* 3.9 24.0 - - + +
631A ILE* 4.8 2.5 - - + -
654A LEU* 3.9 24.7 - - + -
659A ILE* 3.0 32.8 + - + +
660A THR* 4.0 14.5 - - - +
662A LEU* 3.1 32.4 + - + +
663A GLU* 3.3 5.4 + - - +
665A THR* 1.3 74.6 - - - +
667A THR* 1.3 61.0 + - - +
669A LEU* 3.2 31.2 + - + +
670A ARG* 2.8 59.8 + - + +
677A ALA* 6.1 0.4 - - + -
680A TYR* 3.5 43.1 - + - -
681A GLU* 5.5 2.9 - - + -
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Residues in contact with THR 667 (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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663A GLU* 2.8 27.7 + - - +
664A LYS* 3.6 8.2 - - - +
666A TRP* 1.3 77.7 - - - +
668A ALA* 1.3 61.5 + - - +
670A ARG* 3.0 22.7 + - + +
671A HIS* 2.9 51.4 + - + +
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Residues in contact with ALA 668 (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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620A LEU* 4.5 16.8 - - + -
621A GLU* 5.7 4.3 - - + +
624A ALA* 3.8 18.4 - - + -
664A LYS 3.1 17.0 + - - +
665A THR 3.8 5.4 - - - +
666A TRP 3.3 0.2 - - - -
667A THR* 1.3 75.4 - - - +
669A LEU* 1.3 58.3 + - - +
671A HIS* 4.5 4.5 - - - +
672A GLN* 2.9 42.2 + - + +
673A TYR* 4.3 0.2 - - - -
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Residues in contact with LEU 669 (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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624A ALA* 3.7 23.9 - - + +
627A LEU* 4.3 9.2 - - + -
628A SER* 3.7 28.5 - - - +
631A ILE* 3.9 16.4 - - + -
665A THR 3.0 15.4 + - - +
666A TRP* 3.2 38.3 + - + +
668A ALA* 1.3 76.0 - - - +
670A ARG* 1.3 58.1 + - + +
673A TYR* 2.9 48.9 + - + +
676A THR* 4.9 1.3 - - + -
677A ALA* 3.6 24.2 - - + -
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Residues in contact with ARG 670 (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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663A GLU* 3.3 18.7 + - - -
666A TRP* 2.8 45.2 + - + +
667A THR* 3.0 43.3 + - - +
669A LEU* 1.3 73.2 - - + +
671A HIS* 1.3 59.8 + - + +
674A THR* 2.7 33.5 + - - +
677A ALA* 4.1 16.6 - - + -
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Residues in contact with HIS 671 (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 THR* 2.9 49.4 + - + +
668A ALA* 4.1 3.6 - - - +
670A ARG* 1.3 85.2 - - + +
672A GLN* 1.3 79.3 + - - +
674A THR* 3.6 8.6 + - - -
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Residues in contact with GLN 672 (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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621A GLU* 6.5 1.3 - - + -
668A ALA* 2.9 22.3 + - + +
671A HIS* 1.3 95.2 + - - +
673A TYR* 1.3 82.0 + - + +
674A THR* 3.4 5.6 + - - -
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Residues in contact with TYR 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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621A GLU 4.7 1.9 + - - -
624A ALA* 4.1 7.6 - - + -
625A ALA* 3.5 39.5 + - + +
628A SER* 3.5 25.6 - - - +
669A LEU* 2.9 42.0 + - + +
672A GLN* 1.3 95.6 - - + +
674A THR* 1.3 58.0 + - - +
675A GLN 3.3 2.5 - - - -
676A THR* 3.2 8.2 + - - -
677A ALA* 2.9 24.1 + - - +
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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