Contacts of the helix formed by residues 633 - 650 (chain R) in PDB entry 6CNC
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 ASP 633 (chain R).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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630R LEU 4.4 7.7 + - - +
631R ASN 3.1 1.0 - - - -
632R ALA* 1.3 81.9 - - - +
634R PHE* 1.3 63.7 + - - +
636R LEU* 3.1 30.9 - - + +
637R GLU* 3.2 11.6 + - - +
498S PHE* 5.6 3.8 - - - -
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Residues in contact with PHE 634 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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422R PRO* 3.4 43.3 - - + -
423R LYS* 3.4 52.9 - - + +
627R TRP* 5.7 4.5 - + - -
630R LEU 5.1 0.2 + - - -
631R ASN* 3.0 24.4 + - + +
633R ASP* 1.3 76.7 - - - +
635R LEU* 1.3 63.2 + - + +
636R LEU 3.2 0.2 + - - -
637R GLU* 3.3 3.3 + - - +
638R GLN* 2.9 48.5 + - + +
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Residues in contact with LEU 635 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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409R LYS* 5.6 8.1 - - - +
627R TRP* 5.6 9.0 - - + -
628R ILE* 5.5 13.0 - - + -
631R ASN* 2.9 20.2 + - + +
632R ALA* 4.8 3.4 - - - +
634R PHE* 1.3 73.2 - - + +
636R LEU* 1.3 59.9 + - - +
638R GLN* 3.3 35.0 - - + +
639R GLU* 2.9 45.7 + - + +
499S ASN* 5.8 4.0 - - - +
503S ILE* 6.4 1.1 - - + -
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Residues in contact with LEU 636 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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632R ALA 2.6 23.7 + - - +
633R ASP* 3.1 27.6 - - + +
634R PHE 3.1 0.2 - - - -
635R LEU* 1.3 76.9 - - - +
637R GLU* 1.3 55.8 + - + +
640R SER* 2.4 45.7 + - - +
498S PHE* 6.3 1.3 - - + -
502S LEU* 3.5 40.4 - - + -
506S GLN* 3.4 9.8 + - - +
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Residues in contact with GLU 637 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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633R ASP 3.2 10.7 + - - +
634R PHE* 4.2 2.0 - - - +
636R LEU* 1.3 79.8 - - + +
638R GLN* 1.3 66.4 + - - +
640R SER* 3.7 9.4 - - - -
641R LYS* 2.9 27.6 + - + +
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Residues in contact with GLN 638 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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634R PHE* 2.9 43.0 + - + +
635R LEU* 3.3 29.3 - - + +
637R GLU* 1.3 78.6 - - - +
639R GLU* 1.3 58.8 + - - +
641R LYS* 3.3 4.9 + - - +
642R ARG* 2.9 23.9 + - + +
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Residues in contact with GLU 639 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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635R LEU* 2.9 32.1 + - + +
636R LEU 4.2 0.7 - - - +
638R GLN* 1.3 76.2 - - - +
640R SER* 1.3 56.8 + - - +
642R ARG* 2.8 46.8 + - - +
643R LEU* 2.9 25.1 + - - +
503S ILE* 3.1 46.9 - - - +
506S GLN* 3.3 21.0 - - - +
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Residues in contact with SER 640 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132P ARG* 4.8 7.7 + - - -
636R LEU* 2.4 34.7 + - - +
637R GLU* 3.5 12.1 - - - -
638R GLN 3.1 0.2 - - - -
639R GLU* 1.3 76.3 - - - +
641R LYS* 1.3 57.4 + - - +
643R LEU* 2.9 23.4 + - - +
644R LYS* 2.9 12.0 + - - +
506S GLN* 2.7 20.4 + - - +
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Residues in contact with LYS 641 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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637R GLU* 2.9 21.0 + - + +
638R GLN* 3.7 4.3 - - - +
640R SER* 1.3 71.9 - - - +
642R ARG* 1.3 62.0 + - - +
644R LYS* 2.9 38.0 + - + +
645R GLN* 2.9 18.6 + - + +
22X A 5.8 1.8 + - - -
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Residues in contact with ARG 642 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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638R GLN* 2.9 9.7 + - + +
639R GLU* 2.8 58.8 + - - +
641R LYS* 1.3 76.0 - - - +
643R LEU* 1.3 56.8 + - - +
645R GLN* 3.0 47.2 - - - +
646R GLU* 4.1 1.7 + - - +
503S ILE* 5.2 1.2 - - - +
510S LYS* 5.5 9.5 - - - +
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Residues in contact with LEU 643 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132P ARG* 5.1 8.3 - - - +
639R GLU 2.9 11.4 + - - +
640R SER* 2.9 13.6 + - - +
642R ARG* 1.3 74.6 - - - +
644R LYS* 1.3 54.5 + - - +
645R GLN 3.0 2.2 - - - -
646R GLU* 2.7 50.7 + - + +
647R ALA* 3.2 7.4 + - + +
506S GLN* 3.5 36.1 - - + +
509S HIS* 4.9 7.2 - - + -
510S LYS* 3.4 32.3 - - + +
513S MET* 5.1 11.4 - - - -
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Residues in contact with LYS 644 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129P GLU* 4.5 23.8 + - - +
130P SER* 4.9 8.2 + - - +
132P ARG* 3.4 45.7 - - - +
640R SER 2.9 6.4 + - - +
641R LYS* 2.9 35.3 + - + +
643R LEU* 1.3 75.3 - - - +
645R GLN* 1.3 54.6 + - - +
647R ALA* 2.9 5.1 + - + +
648R ASP* 2.8 40.9 + - - +
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Residues in contact with GLN 645 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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641R LYS* 2.9 19.9 + - + +
642R ARG* 3.0 37.6 - - - +
644R LYS* 1.3 76.3 - - - +
646R GLU* 1.3 61.6 + - - +
648R ASP* 3.2 31.4 - - - +
649R ILE* 4.3 4.0 + - - +
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Residues in contact with GLU 646 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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642R ARG 4.1 1.4 + - - +
643R LEU* 2.7 23.0 + - + +
645R GLN* 1.3 70.5 - - - +
647R ALA* 1.3 62.7 + - - +
648R ASP 3.0 6.2 + - - -
649R ILE* 3.3 17.3 + - - +
650R ALA* 3.7 6.8 + - - +
510S LYS* 3.2 44.0 - - - +
513S MET* 6.3 1.6 - - - -
514S LYS* 4.5 21.8 + - - +
517S GLU* 5.6 2.1 - - - +
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Residues in contact with ALA 647 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132P ARG* 3.7 15.5 - - - +
151P TYR* 2.8 34.8 + - - +
643R LEU* 3.2 3.5 + - + +
644R LYS* 2.9 26.5 + - + +
646R GLU* 1.3 77.1 - - - +
648R ASP* 1.3 63.5 + - - +
649R ILE 3.5 0.2 - - - -
650R ALA* 3.4 16.7 + - - +
513S MET* 4.0 13.2 - - + -
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Residues in contact with ASP 648 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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644R LYS* 2.8 33.0 + - - +
645R GLN* 3.2 25.7 - - - +
646R GLU 3.0 0.4 + - - -
647R ALA* 1.3 79.2 - - - +
649R ILE* 1.3 67.3 + - + +
650R ALA 4.0 4.2 - - - -
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Residues in contact with ILE 649 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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645R GLN 5.1 3.4 - - - +
646R GLU* 3.3 9.2 + - - +
648R ASP* 1.3 81.2 - - + +
650R ALA* 1.3 62.6 + - - +
517S GLU* 5.3 8.0 - - - +
520S LYS* 4.5 2.6 + - - -
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Residues in contact with ALA 650 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135P LYS* 4.8 11.2 - - - +
151P TYR* 4.0 23.6 - - + +
154P GLN* 5.0 0.9 - - - +
646R GLU* 3.7 5.5 + - + +
647R ALA* 3.6 25.1 - - - +
648R ASP 3.2 4.8 - - - -
649R ILE* 1.3 83.8 - - - +
513S MET* 5.7 6.5 - - + +
517S GLU* 4.7 24.1 + - + +
520S LYS* 2.3 35.9 + - + +
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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