Contacts of the helix formed by residues 632 - 646 (chain A) in PDB entry 3RTR
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 LYS 632 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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551A CYS* 4.4 13.6 + - + +
552A THR* 4.9 3.9 + - - +
626A THR* 4.9 2.0 - - - -
630A GLN 3.6 5.1 + - - -
631A ILE* 1.3 69.1 - - - +
633A MET* 1.3 55.7 + - - +
634A ASP* 3.2 38.5 + - + +
635A ILE* 2.8 23.5 + - + +
636A LEU 2.7 29.8 + - - -
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Residues in contact with MET 633 (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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622A VAL* 3.3 33.2 - - + +
623A GLN* 3.5 35.4 - - - +
626A THR* 3.0 34.1 - - + +
631A ILE 3.0 3.4 + - - -
632A LYS* 1.3 73.2 - - - +
634A ASP* 1.3 62.5 + - - +
636A LEU* 3.6 10.8 - - + -
637A ALA* 2.8 33.4 + - + +
663A LEU 6.1 0.2 - - - +
665A PRO* 4.1 16.8 - - + -
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Residues in contact with ASP 634 (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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632A LYS* 3.0 36.1 + - + +
633A MET* 1.3 82.6 - - - +
635A ILE* 1.3 61.8 + - + +
637A ALA* 4.3 2.9 - - - +
638A GLN* 3.2 34.4 + - - +
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Residues in contact with ILE 635 (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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551A CYS* 4.1 22.0 - - + -
606A PHE* 4.3 17.5 - - + -
631A ILE* 3.5 20.6 - - + -
632A LYS* 2.8 22.4 + - + +
634A ASP* 1.3 79.6 - - + +
636A LEU* 1.3 65.2 + - - +
637A ALA 3.3 0.2 - - - -
638A GLN* 3.1 9.2 + - - +
639A VAL* 3.0 41.1 + - + +
688A MET* 4.8 17.0 - - + -
694A GLN* 5.1 9.6 - - - +
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Residues in contact with LEU 636 (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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610A ILE* 3.6 31.2 - - + -
622A VAL* 3.5 26.2 - - + +
625A LEU* 4.0 11.0 - - + -
626A THR* 3.2 33.9 - - - +
629A THR* 4.1 17.5 - - - +
631A ILE* 3.8 14.5 - - + +
632A LYS 2.7 17.0 + - - +
633A MET* 3.8 7.0 - - + -
635A ILE* 1.3 73.4 - - - +
637A ALA* 1.3 63.0 + - - +
639A VAL* 3.8 4.1 - - - +
640A LEU* 2.9 39.0 + - + +
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Residues in contact with ALA 637 (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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622A VAL* 5.9 5.1 - - + +
633A MET* 2.8 23.1 + - + +
634A ASP* 4.3 3.6 - - - +
636A LEU* 1.3 73.8 - - - +
638A GLN* 1.3 59.1 + - + +
640A LEU* 3.3 7.7 + - - +
641A GLN* 2.8 31.5 + - - +
663A LEU* 4.4 28.1 - - + +
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Residues in contact with GLN 638 (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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634A ASP* 3.2 22.0 + - - +
635A ILE* 3.1 10.6 + - - +
637A ALA* 1.3 77.7 - - + +
639A VAL* 1.3 59.5 - - - +
641A GLN* 3.5 12.9 - - - +
642A ILE* 3.4 22.2 + - - +
688A MET* 2.9 42.9 - - + +
689A LYS 6.0 0.4 - - - +
690A THR* 2.7 33.1 + - + +
694A GLN* 4.5 11.2 + - - +
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Residues in contact with VAL 639 (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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606A PHE* 4.4 20.9 - - + -
607A GLN* 3.8 17.9 - - + +
610A ILE* 4.1 17.0 - - + -
631A ILE* 5.7 1.6 - - + -
635A ILE* 3.0 31.6 + - + +
636A LEU* 3.8 5.8 - - - +
638A GLN* 1.3 75.2 - - - +
640A LEU* 1.3 61.7 + - - +
642A ILE* 2.8 20.9 + - - +
643A LEU* 2.9 35.6 + - + +
688A MET* 4.0 15.5 - - - -
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Residues in contact with LEU 640 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
610A ILE* 4.3 28.9 - - + -
622A VAL* 4.0 19.7 - - + -
625A LEU* 4.7 9.9 - - + -
636A LEU* 2.9 37.4 + - + +
637A ALA* 3.5 4.5 - - - +
639A VAL* 1.3 71.1 - - - +
641A GLN* 1.3 53.7 + - - +
642A ILE 2.7 6.4 + - - -
643A LEU* 2.6 25.4 + - + +
644A LEU* 2.8 21.0 + - + +
649A LEU* 4.4 16.4 - - + -
663A LEU* 3.6 26.2 - - + -
669A ILE* 4.1 16.2 - - + -
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Residues in contact with GLN 641 (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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637A ALA 2.8 22.2 + - - +
638A GLN* 3.5 14.4 - - - +
639A VAL 3.2 0.2 - - - -
640A LEU* 1.3 71.0 - - - +
642A ILE* 1.3 58.2 + - + +
644A LEU* 4.3 3.1 - - - +
645A LYS* 3.2 30.2 + - - +
658A VAL* 4.1 29.2 - - + +
659A ASP* 4.2 30.5 + - - +
661A VAL 5.2 1.0 - - - +
663A LEU* 4.7 11.7 - - + +
689A LYS* 4.5 20.8 - - - +
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Residues in contact with ILE 642 (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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607A GLN* 3.3 25.8 - - - +
638A GLN 3.4 12.2 + - - +
639A VAL* 2.8 11.5 + - - +
640A LEU 2.7 5.1 + - - -
641A GLN* 1.3 75.4 - - + +
643A LEU* 1.3 61.5 + - - +
644A LEU 3.2 2.7 + - - -
645A LYS* 3.4 6.7 + - - +
646A SER* 3.4 19.6 + - - -
684A ILE* 3.7 8.7 - - + +
686A VAL* 3.2 36.1 - - + +
687A PRO 3.2 30.3 - - - +
688A MET* 3.9 15.3 - - + -
689A LYS 5.7 0.2 - - - +
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Residues in contact with LEU 643 (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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607A GLN* 3.4 38.4 - - + +
610A ILE* 5.3 4.9 - - + -
611A LEU* 3.7 29.6 - - + -
639A VAL* 2.9 33.2 + - + +
640A LEU* 2.6 19.0 + - + +
642A ILE* 1.3 73.4 - - - +
644A LEU* 1.3 51.5 + - + +
646A SER* 2.7 28.3 + - - +
648A LEU* 4.1 19.5 + - + +
649A LEU* 3.5 35.6 + - + -
684A ILE* 4.3 12.3 - - + -
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Residues in contact with LEU 644 (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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640A LEU* 2.8 20.4 + - + +
641A GLN* 4.5 0.4 - - - -
643A LEU* 1.3 74.8 - - + +
645A LYS* 1.3 61.3 + - - +
646A SER 2.5 18.4 - - - +
647A LYS* 4.4 1.9 - - - +
649A LEU* 3.5 36.7 - - + +
650A VAL* 4.1 4.3 - - - +
651A LEU* 3.6 39.7 - - + -
658A VAL* 3.4 37.5 - - + +
663A LEU* 4.1 24.7 - - + -
669A ILE* 4.5 8.3 - - + -
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Residues in contact with LYS 645 (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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641A GLN* 3.2 25.7 + - - +
642A ILE* 3.4 7.6 + - - +
644A LEU* 1.3 77.3 - - - +
646A SER* 1.3 60.6 + - - +
647A LYS* 3.7 6.4 + - - +
657A ASN* 5.4 1.3 - - - -
658A VAL* 3.7 30.7 - - + +
659A ASP* 3.9 29.4 + - - +
689A LYS* 5.8 4.4 - - - +
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Residues in contact with SER 646 (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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642A ILE* 3.4 7.9 + - - -
643A LEU* 2.7 33.8 + - - +
644A LEU 2.5 19.6 - - - +
645A LYS* 1.3 77.9 - - - +
647A LYS* 1.3 56.7 + - - +
648A LEU* 3.0 19.0 + - - +
649A LEU 3.8 0.3 - - - +
675A TYR* 5.2 3.8 - - - -
682A VAL* 6.3 0.2 - - - -
684A ILE* 4.1 24.9 - - - +
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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