Contacts of the helix formed by residues 631 - 641 (chain O) in PDB entry 6LTJ
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 631 (chain O).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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529O SER 4.5 8.3 + - - -
530O HIS* 5.1 1.2 - - - +
531O PHE 3.7 17.4 + - - +
532O HIS* 3.6 25.8 - - + +
533O VAL* 5.0 0.9 - - + +
624O SER* 4.0 3.1 - - - -
630O ARG* 1.3 78.3 - - - +
632O GLN* 1.3 70.8 + - + +
633O ASP* 3.4 21.1 - - - +
634O GLU* 2.6 30.7 + - - -
635O CYS* 3.1 24.3 + - - -
79R TRP* 4.1 9.5 - - - -
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Residues in contact with GLN 632 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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532O HIS* 3.5 33.6 + - - +
533O VAL 5.4 1.6 - - - +
534O LEU* 5.1 1.7 - - - +
620O TRP* 3.4 24.0 - - + +
621O ASN* 2.3 46.3 + - - +
624O SER* 3.6 13.5 + - - +
631O THR* 1.3 77.5 - - + +
633O ASP* 1.3 63.1 + - - +
635O CYS* 3.2 5.0 + - - +
636O ILE* 3.0 35.5 + - - +
495P PHE* 3.6 36.6 - - + -
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Residues in contact with ASP 633 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
533O VAL* 4.2 19.4 + - - +
631O THR* 3.4 16.6 - - - +
632O GLN* 1.3 79.9 - - - +
634O GLU* 1.3 57.9 + - + +
636O ILE* 3.4 8.9 + - - +
637O LEU* 2.9 40.0 + - + +
488P GLN* 6.2 2.9 - - + -
491P VAL* 4.4 15.4 - - + +
492P CYS* 4.5 22.8 - - - -
495P PHE* 4.8 13.7 - - - +
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Residues in contact with GLU 634 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
598O THR* 3.1 38.1 + - - +
601O TRP* 3.8 5.9 + - + +
630O ARG* 3.6 21.8 + - + +
631O THR* 2.6 45.1 + - - +
632O GLN 3.3 0.2 - - - -
633O ASP* 1.3 78.3 - - - +
635O CYS* 1.3 58.4 + - - +
637O LEU* 3.9 7.2 - - + +
638O HIS* 2.9 32.7 + - - +
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Residues in contact with CYS 635 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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601O TRP* 4.1 10.1 - - - -
609O LEU* 3.9 17.6 - - + +
620O TRP* 4.3 13.0 - - + -
623O VAL* 4.5 2.0 - - + -
624O SER* 4.3 13.7 - - - +
627O VAL* 4.1 24.2 - - - -
630O ARG* 3.9 16.4 - - - -
631O THR 3.1 19.2 + - - +
632O GLN* 3.2 9.9 + - - +
634O GLU* 1.3 78.7 - - - +
636O ILE* 1.3 62.0 + - - +
638O HIS 3.8 0.3 - - - -
639O PHE* 2.9 26.2 + - - +
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Residues in contact with ILE 636 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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416I LEU* 5.0 2.0 - - + -
420I VAL* 5.6 0.4 - - + -
620O TRP* 3.5 45.1 - - + -
632O GLN 3.0 20.7 + - - +
633O ASP* 3.9 7.4 - - - +
635O CYS* 1.3 75.4 - - - +
637O LEU* 1.3 64.8 + - - +
639O PHE* 3.3 2.1 + - - +
640O LEU* 2.9 40.2 + - + +
491P VAL* 4.0 27.1 - - + -
494P TYR* 4.2 21.3 - - + -
495P PHE* 4.0 29.6 - - + -
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Residues in contact with LEU 637 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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633O ASP* 2.9 26.5 + - + +
634O GLU* 3.9 7.9 - - + +
636O ILE* 1.3 76.3 - - - +
638O HIS* 1.3 63.4 + - - +
640O LEU* 3.2 7.9 + - + +
641O ARG* 3.1 66.2 + - + +
487P ALA* 4.2 17.7 - - + +
488P GLN* 4.4 20.9 - - + -
491P VAL* 3.7 28.5 - - + -
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Residues in contact with HIS 638 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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601O TRP* 3.5 48.4 - + + +
606O THR* 3.5 30.4 + - + -
609O LEU* 3.4 17.8 - - - +
634O GLU 2.9 18.4 + - - +
635O CYS 4.1 1.3 - - - +
637O LEU* 1.3 76.9 - - - +
639O PHE* 1.3 60.3 + - - +
641O ARG* 3.6 8.8 + - + +
642O LEU* 3.3 46.2 + - + +
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Residues in contact with PHE 639 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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409I LEU* 3.9 16.2 - - + -
412I PHE* 3.3 39.5 - + - -
413I GLN* 2.9 55.5 + - + -
416I LEU* 4.5 7.9 - - + -
609O LEU* 4.3 4.5 - - + +
610O LEU* 4.6 3.8 - - + -
613O LEU* 3.7 30.7 - - + -
620O TRP* 4.0 14.1 - + + -
635O CYS 2.9 18.3 + - - +
636O ILE* 3.7 4.0 - - - +
638O HIS* 1.3 76.9 + - - +
640O LEU* 1.3 63.4 + - + +
642O LEU* 3.2 26.5 + - + +
644O ILE* 4.4 5.4 - - + -
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Residues in contact with LEU 640 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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413I GLN* 3.0 4.6 + - + +
416I LEU* 3.7 35.4 - - + +
417I ARG* 2.6 58.0 + - + +
420I VAL* 4.4 17.7 - - + -
636O ILE* 2.9 26.3 + - + +
637O LEU* 3.2 8.0 + - + +
639O PHE* 1.3 81.2 - - + +
641O ARG* 1.3 53.8 + - + +
642O LEU 3.4 0.4 - - - -
482P TYR* 4.2 23.0 - - + -
491P VAL* 4.0 24.9 - - + -
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Residues in contact with ARG 641 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
417I ARG* 4.1 4.0 - - - +
637O LEU* 3.1 46.7 + - - +
638O HIS* 3.6 8.5 + - + +
639O PHE 3.1 1.2 - - - -
640O LEU* 1.3 77.9 - - + +
642O LEU* 1.3 63.8 + - - +
643O PRO* 3.2 9.7 - - - +
479P ALA* 3.6 11.5 - - - +
482P TYR* 2.7 36.1 + - + +
483P PHE* 3.5 53.9 - - + +
484P GLN 5.1 0.6 + - - -
487P ALA* 3.9 17.0 - - - +
488P GLN* 5.2 1.4 - - - +
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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