Contacts of the helix formed by residues 611 - 620 (chain A) in PDB entry 2P2Q
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 MET 611 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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603A PRO* 2.7 40.0 + - + +
604A LYS 4.5 1.6 - - - +
605A THR* 4.6 18.8 - - - +
609A LYS* 5.3 1.1 - - - +
610A ILE* 1.3 68.1 - - - +
612A ARG* 1.3 63.0 + - - +
613A ARG 3.3 3.1 + - - +
614A ILE* 3.7 24.4 + - + -
615A LEU* 3.4 22.9 + - - +
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Residues in contact with ARG 612 (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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518A ASP* 3.0 35.6 + - - -
529A THR* 3.7 12.9 + - - +
533A GLU* 2.9 28.7 + - - -
546A ALA* 4.5 6.7 - - - +
547A VAL 2.9 25.5 + - - +
548A VAL* 4.0 9.9 - - + +
610A ILE* 2.9 38.4 + - + +
611A MET* 1.3 71.0 - - - +
613A ARG* 1.3 60.1 + - - +
615A LEU* 3.5 11.1 + - + +
616A ARG* 3.0 47.9 + - - +
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Residues in contact with ARG 613 (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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611A MET* 3.3 1.4 - - + +
612A ARG* 1.3 75.5 - - - +
614A ILE* 1.3 67.5 + - + +
616A ARG* 3.4 19.3 + - - +
617A LYS* 3.0 23.0 + - - +
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Residues in contact with ILE 614 (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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603A PRO* 4.0 13.0 - - + -
611A MET* 3.7 33.5 + - + +
612A ARG 3.4 0.2 - - - -
613A ARG* 1.3 79.7 - - + +
615A LEU* 1.3 61.1 + - - +
617A LYS* 3.2 7.2 + - - +
618A ILE* 2.8 67.1 + - + +
638A VAL* 4.0 29.2 - - + -
641A LEU* 4.1 13.7 - - + -
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Residues in contact with LEU 615 (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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546A ALA* 3.8 22.0 - - + -
548A VAL* 4.0 7.6 - - + -
562A TYR* 2.7 56.8 + - + -
602A LEU* 4.3 3.4 - - + -
603A PRO* 3.5 28.0 - - + -
610A ILE* 3.7 23.6 - - + -
611A MET 3.4 17.3 - - - +
612A ARG* 3.5 11.9 + - + +
613A ARG 3.3 0.2 - - - -
614A ILE* 1.3 77.4 - - - +
616A ARG* 1.3 55.5 + - - +
618A ILE* 4.7 1.6 - - + -
619A ALA* 2.9 19.4 + - - +
641A LEU* 4.0 12.6 - - + -
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Residues in contact with ARG 616 (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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518A ASP* 3.4 24.2 + - - -
548A VAL* 3.9 18.8 - - + +
549A GLY 4.3 19.1 + - - +
612A ARG* 3.0 41.0 + - - +
613A ARG* 3.5 28.3 - - - +
615A LEU* 1.3 76.9 - - - +
617A LYS* 1.3 62.0 + - - +
619A ALA* 3.8 2.3 - - - +
620A ALA* 3.2 23.3 + - + +
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Residues in contact with LYS 617 (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 ARG 3.0 17.8 + - - +
614A ILE* 3.6 6.5 - - - +
616A ARG* 1.3 75.7 - - - +
618A ILE* 1.3 60.9 + - + +
620A ALA* 3.2 10.3 + - - +
622A ASP* 2.7 48.3 - - - +
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Residues in contact with ILE 618 (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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562A TYR* 3.6 15.0 - - + +
614A ILE* 2.8 47.5 + - + +
615A LEU* 5.4 0.2 - - - -
617A LYS* 1.3 71.7 - - + +
619A ALA* 1.3 63.9 + - - +
621A GLY* 3.0 15.1 + - - -
622A ASP 3.9 10.0 + - - +
638A VAL* 3.9 16.8 - - + +
641A LEU* 3.8 33.0 - - + +
642A LEU* 4.3 20.6 - - + +
645A LYS* 3.7 32.1 - - + +
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Residues in contact with ALA 619 (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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548A VAL* 3.6 16.8 - - + -
550A ILE* 3.3 32.8 - - + +
560A TYR* 3.7 24.8 - - + -
562A TYR* 3.2 10.6 + - - +
615A LEU 2.9 22.1 + - - +
616A ARG 3.8 2.0 - - - +
617A LYS 3.4 0.2 - - - -
618A ILE* 1.3 72.2 - - - +
620A ALA* 1.3 56.7 + - - +
621A GLY 3.2 4.0 + - - -
645A LYS* 3.6 13.7 + - - +
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Residues in contact with ALA 620 (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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550A ILE* 3.9 7.4 - - + +
551A PRO* 4.3 22.4 - - + -
616A ARG* 3.2 16.4 + - + +
617A LYS* 3.6 7.6 - - - +
618A ILE 3.2 1.0 - - - -
619A ALA* 1.3 74.0 - - - +
621A GLY* 1.3 62.3 + - - +
622A ASP* 3.3 9.7 + - + +
645A LYS* 5.1 0.2 - - - -
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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