Contacts of the helix formed by residues 662 - 673 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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613D ILE* 4.1 22.7 - - + -
614D LEU* 3.7 24.9 - - + -
623D ARG* 5.0 5.2 - - - +
658D GLN 3.7 6.3 - - - +
659D ILE* 3.4 21.1 - - + +
660D THR 3.1 2.4 - - - -
661D ARG* 1.3 74.2 - - + +
663D GLU* 1.3 53.4 + - - +
664D LYS 3.3 3.1 - - - -
665D THR* 3.0 21.8 + - + +
666D TRP* 2.8 38.2 + - + -
812D SER* 3.3 33.9 - - - +
815D LEU* 5.0 4.9 - - + -
816D GLU* 3.6 20.2 - - + +
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Residues in contact with GLU 663 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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660D THR 4.5 7.1 - - - +
661D ARG* 2.6 16.3 + - - +
662D LEU* 1.3 71.4 - - - +
664D LYS* 1.3 57.4 + - + +
666D TRP* 4.4 5.4 - - - +
667D THR* 2.6 48.8 + - - +
670D ARG* 4.4 15.7 + - - -
816D GLU* 3.4 2.5 + - - +
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Residues in contact with LYS 664 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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620D LEU* 3.7 22.4 - - + +
623D ARG* 5.9 0.2 - - - +
663D GLU* 1.3 78.8 - - + +
665D THR* 1.3 57.5 + - - +
667D THR* 3.4 6.0 + - - -
668D ALA* 2.9 28.8 + - - +
815D LEU 5.6 0.6 + - - -
816D GLU* 3.2 37.9 + - + +
817D PRO* 4.9 11.5 + - - +
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Residues in contact with THR 665 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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613D ILE* 5.2 5.4 - - + -
620D LEU* 3.5 7.1 - - - +
623D ARG* 3.0 62.1 + - + +
624D ALA* 3.8 13.4 - - - +
627D LEU* 4.5 12.1 - - + -
662D LEU* 3.0 18.2 + - + +
664D LYS* 1.3 75.3 - - - +
666D TRP* 1.3 58.7 + - - +
668D ALA* 3.0 6.3 + - - +
669D LEU* 2.9 26.9 + - - +
816D GLU* 3.1 6.8 + - - -
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Residues in contact with TRP 666 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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627D LEU* 3.5 38.8 - - + -
631D ILE* 4.7 2.2 - - + -
654D LEU* 3.7 25.8 - - + -
659D ILE* 2.9 33.8 + - + +
660D THR* 3.6 21.4 - - + +
662D LEU* 2.8 31.1 + - + +
663D GLU* 4.0 7.4 - - - +
665D THR* 1.3 73.4 - - - +
667D THR* 1.3 56.5 + - - +
669D LEU* 3.5 24.1 + - + +
670D ARG* 2.8 62.1 + - - +
680D TYR* 3.9 37.0 - + - -
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Residues in contact with THR 667 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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663D GLU* 2.6 41.8 + - - +
664D LYS* 3.7 5.8 - - - -
666D TRP* 1.3 74.0 - - - +
668D ALA* 1.3 67.1 + - - +
670D ARG* 3.3 13.0 + - - +
671D HIS* 3.0 61.3 + - + +
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Residues in contact with ALA 668 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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620D LEU* 4.4 17.3 - - + +
621D GLU* 5.6 1.3 - - + -
624D ALA* 3.7 17.5 - - + -
664D LYS 2.9 14.9 + - - +
665D THR* 3.2 11.7 - - - +
667D THR* 1.3 77.2 - - - +
669D LEU* 1.3 61.2 + - - +
671D HIS* 3.3 7.0 + - - -
672D GLN* 3.0 38.9 + - - +
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Residues in contact with LEU 669 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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624D ALA* 3.9 12.9 - - + +
627D LEU* 4.1 13.5 - - + -
628D SER* 3.7 40.6 - - - +
631D ILE* 4.1 5.6 - - + -
665D THR 2.9 12.4 + - - +
666D TRP* 3.6 39.5 - - + +
667D THR 3.3 0.2 - - - -
668D ALA* 1.3 72.4 - - - +
670D ARG* 1.3 62.0 + - + +
673D TYR* 2.7 45.9 + - + -
676D THR* 4.4 6.3 - - + -
677D ALA* 3.3 31.2 - - + -
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Residues in contact with ARG 670 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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663D GLU* 4.4 11.6 + - - -
666D TRP* 2.8 65.1 + - - +
667D THR* 3.3 20.3 + - - +
669D LEU* 1.3 76.3 - - + +
671D HIS* 1.3 63.1 + - + +
674D THR* 2.4 35.7 + - - +
677D ALA* 4.0 20.0 - - + -
681D GLU* 5.1 11.3 + - - +
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Residues in contact with HIS 671 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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667D THR* 3.0 43.0 + - + +
668D ALA* 3.8 6.5 - - - +
670D ARG* 1.3 89.8 - - + +
672D GLN* 1.3 63.9 + - + +
674D THR* 3.7 7.0 + - - -
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Residues in contact with GLN 672 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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621D GLU* 4.6 23.8 - - - +
624D ALA* 4.1 8.8 - - - +
668D ALA* 3.0 24.7 + - - +
671D HIS* 1.3 83.4 - - + +
673D TYR* 1.3 92.0 + - + +
674D THR* 3.5 3.1 + - - -
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Residues in contact with TYR 673 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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621D GLU 4.7 1.6 + - - -
624D ALA* 3.9 5.4 - - + -
625D ALA* 3.6 39.6 + - - +
628D SER* 3.5 33.4 - - - +
669D LEU* 2.7 33.9 + - + +
672D GLN* 1.3 102.6 + - + +
674D THR* 1.3 63.9 + - - +
675D GLN* 3.2 3.4 - - - -
676D THR* 2.9 17.2 + - - +
677D ALA* 2.9 9.5 + - - +
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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