Contacts of the helix formed by residues 610 - 621 (chain A) in PDB entry 2O1X
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 610 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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519A TYR* 3.6 28.5 - - + +
601A GLU* 4.2 3.3 - - - +
604A HIS* 3.6 7.3 + - + +
605A ALA* 3.3 33.8 + - - +
609A ILE* 1.3 83.4 - - - +
611A ALA* 1.3 60.8 + - - +
612A PRO* 3.7 13.4 - - + +
613A ALA* 2.9 22.3 + - - +
614A ILE* 2.8 27.8 + - - +
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Residues in contact with ALA 611 (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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519A TYR* 3.9 20.6 - - + +
522A LYS* 3.9 33.0 - - + -
523A ALA* 4.0 14.9 - - - +
610A ASP* 1.3 74.8 - - - +
612A PRO* 1.3 72.4 - - + +
613A ALA 2.9 0.5 + - - -
614A ILE* 3.0 4.1 + - - +
615A ARG* 2.8 26.4 + - + +
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Residues in contact with PRO 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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610A ASP* 3.7 15.7 - - - +
611A ALA* 1.3 95.1 - - + +
613A ALA* 1.3 54.6 + - - +
615A ARG* 3.3 12.7 + - + +
616A THR* 2.9 31.3 + - - -
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Residues in contact with ALA 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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605A ALA 4.7 2.9 - - - +
608A GLY* 3.4 34.8 - - - +
610A ASP* 2.9 23.9 + - - +
612A PRO* 1.3 76.6 - - - +
614A ILE* 1.3 65.3 + - - +
616A THR* 3.1 9.4 + - - -
617A VAL* 3.1 26.9 + - - +
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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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510A ILE* 3.8 22.2 - - + -
519A TYR* 3.7 27.4 - - + +
520A ALA* 4.0 3.8 - - - +
523A ALA* 3.6 17.7 - - + -
557A ILE* 4.4 9.6 - - + -
559A VAL* 4.2 14.4 - - + -
588A LEU* 3.7 20.9 - - + -
609A ILE 3.1 26.0 - - - +
610A ASP 2.8 16.3 + - - +
611A ALA 3.7 3.8 - - - +
613A ALA* 1.3 68.3 - - - +
615A ARG* 1.3 61.5 + - - +
617A VAL* 3.1 9.2 + - - +
618A LEU* 2.8 34.4 + - + +
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Residues in contact with ARG 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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522A LYS* 4.8 3.2 + - - +
523A ALA* 3.2 34.7 + - - +
525A GLU* 4.5 6.1 - - - +
526A ASP* 3.8 28.1 + - - +
527A LEU* 3.9 10.9 - - + +
611A ALA* 2.8 15.6 + - - +
612A PRO* 3.3 15.3 - - + +
614A ILE* 1.3 77.1 - - - +
616A THR* 1.3 60.5 + - - +
618A LEU* 3.4 11.2 + - + +
619A ALA* 3.0 21.5 + - - +
625A VAL* 3.5 25.4 - - + +
626A PRO* 3.3 37.3 + - - +
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Residues in contact with THR 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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612A PRO 2.9 16.7 + - - -
613A ALA* 3.4 12.1 - - - -
614A ILE 3.1 0.4 - - - -
615A ARG* 1.3 73.4 - - - +
617A VAL* 1.3 66.4 + - + +
619A ALA* 3.0 11.4 + - + +
620A GLU* 3.0 35.7 + - + +
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Residues in contact with VAL 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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557A ILE* 3.9 20.9 - - + -
586A ARG* 3.9 37.9 - - + +
588A LEU* 3.9 27.8 - - + -
608A GLY 5.4 0.9 - - - +
613A ALA 3.1 14.9 + - - +
614A ILE* 3.5 8.3 - - - +
616A THR* 1.3 75.2 - - - +
618A LEU* 1.3 62.0 + - - +
620A GLU* 3.0 26.4 + - - +
621A LEU* 3.1 15.6 + - + +
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Residues in contact with LEU 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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508A VAL* 3.7 27.1 - - + -
510A ILE* 4.5 5.2 - - + -
523A ALA* 4.2 8.5 - - + +
527A LEU* 3.7 23.3 - - + -
530A VAL* 3.7 30.1 - - + -
557A ILE* 3.9 8.1 - - + -
614A ILE* 2.8 39.2 + - + +
615A ARG* 3.4 14.6 - - - +
617A VAL* 1.3 70.6 - - - +
619A ALA* 1.3 60.8 + - - +
621A LEU* 3.4 9.9 + - - -
623A VAL* 3.0 36.1 + - + +
625A VAL* 4.1 8.3 - - + -
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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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615A ARG 3.0 11.3 + - - +
616A THR* 3.0 14.1 + - + +
618A LEU* 1.3 75.1 - - - +
620A GLU* 1.3 58.3 + - - +
622A GLY* 2.9 21.8 + - - -
623A VAL 3.6 13.3 + - - +
625A VAL* 3.8 15.8 - - + +
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Residues in contact with GLU 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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586A ARG* 2.3 42.4 + - - +
616A THR* 3.0 24.5 + - + +
617A VAL* 3.0 20.0 + - - +
619A ALA* 1.3 75.9 - - - +
621A LEU* 1.3 59.1 + - - +
622A GLY* 3.2 3.1 + - - -
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Residues in contact with LEU 621 (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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508A VAL* 4.2 23.3 - - + -
554A ARG* 2.6 32.3 + - - +
555A ALA* 4.3 13.5 - - + -
556A LEU 5.1 0.7 - - - +
557A ILE* 4.0 32.1 - - + -
584A THR* 4.1 22.4 - - + -
586A ARG* 3.8 33.0 - - + +
617A VAL* 3.1 21.7 + - + +
618A LEU* 4.0 5.2 - - - +
619A ALA 3.2 0.8 - - - -
620A GLU* 1.3 75.0 - - - +
622A GLY* 1.3 52.7 + - - +
623A VAL 3.5 1.1 - - - -
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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