Contacts of the helix formed by residues 616 - 628 (chain J) in PDB entry 1O1F
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 VAL 616 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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350J ALA* 4.5 23.6 - - + -
353J MLY 3.7 22.9 - - + -
354J LEU* 5.0 6.1 - - + -
389J LEU 4.4 4.5 - - - +
390J MET 3.4 32.3 - - - +
391J GLY* 3.6 7.9 - - - +
614J SER* 3.0 3.1 + - - -
615J SER* 1.3 80.5 - - - +
617J MLY 1.3 53.7 - - - +
618J THR* 3.2 1.3 - - - +
619J LEU* 2.7 40.1 + - + +
620J ALA 3.0 7.8 + - - -
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Residues in contact with MLY 617 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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346J ASP* 5.4 10.5 - - - +
614J SER 5.0 2.0 - - - +
615J SER 3.5 7.0 + - - +
616J VAL* 1.3 70.8 + - - +
618J THR* 1.3 55.0 + - - +
620J ALA* 2.8 12.8 + - - +
621J LEU* 2.6 48.2 + - + +
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Residues in contact with THR 618 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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346J ASP* 5.1 4.5 + - - -
347J GLU* 4.0 19.1 + - - +
350J ALA* 3.7 28.1 - - + +
354J LEU* 4.4 7.2 - - + -
437J MET* 6.3 0.4 - - + -
440J TRP* 3.6 36.1 - - + -
616J VAL* 3.2 1.7 - - - -
617J MLY 1.3 79.3 + - - +
619J LEU* 1.3 63.9 + - - +
621J LEU* 2.9 13.8 + - - +
622J LEU* 2.8 31.3 + - + +
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Residues in contact with LEU 619 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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354J LEU* 4.6 13.2 - - + +
390J MET* 3.6 40.6 - - + +
392J LEU* 4.9 0.7 - - + -
433J VAL* 4.5 11.7 - - + -
611J TYR* 3.9 29.5 - - + +
614J SER* 3.9 9.2 - - - +
616J VAL* 2.7 24.1 + - + +
618J THR* 1.3 77.8 - - - +
620J ALA* 1.3 66.2 + - - +
621J LEU 3.3 0.2 + - - -
622J LEU* 3.5 28.6 + - + +
623J PHE* 3.7 25.6 + - + +
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Residues in contact with ALA 620 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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611J TYR 3.5 20.2 + - - +
612J GLN* 4.2 16.1 - - - +
613J MLY 5.4 0.2 - - - -
614J SER* 4.4 11.0 - - - +
616J VAL 3.0 6.1 + - - +
617J MLY 2.8 22.4 + - - +
619J LEU* 1.3 78.5 - - - +
621J LEU* 1.3 66.1 + - + +
623J PHE* 3.2 12.8 + - - +
624J ALA* 3.6 7.8 + - - +
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Residues in contact with LEU 621 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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440J TRP* 5.2 14.4 - - + +
617J MLY 2.6 28.8 + - + +
618J THR* 2.9 11.7 + - - +
620J ALA* 1.3 78.4 - - + +
622J LEU* 1.3 58.3 + - + +
623J PHE 2.8 11.3 + - - -
624J ALA* 3.0 26.4 + - + +
625J THR* 5.3 0.5 - - - +
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Residues in contact with LEU 622 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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354J LEU* 4.9 7.9 - - + -
433J VAL* 4.3 10.8 - - + +
436J MLY 3.5 34.9 - - + +
437J MET* 4.0 29.4 - - + +
440J TRP* 4.2 22.9 - - + -
618J THR* 2.8 36.8 + - + +
619J LEU* 3.7 27.6 - - + +
620J ALA 3.4 0.2 - - - -
621J LEU* 1.3 80.0 - - + +
623J PHE* 1.5 57.1 + - + +
624J ALA 3.7 0.2 - - - -
625J THR* 4.1 9.2 - - - +
626J TYR* 4.0 5.0 - - - -
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Residues in contact with PHE 623 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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429J LEU* 5.4 0.9 - - + -
432J ALA* 4.2 7.6 - - + -
433J VAL* 3.7 39.3 - - + -
436J MLY 4.0 13.5 - - + -
603J LEU* 4.6 0.4 - - + -
608J ILE* 3.7 36.1 - - + -
611J TYR* 3.2 39.5 - + + -
612J GLN* 3.2 19.2 + - + +
619J LEU* 4.1 13.0 - - + +
620J ALA 3.2 8.9 + - - +
621J LEU 2.8 6.5 + - - -
622J LEU* 1.5 70.7 - - + +
624J ALA* 1.3 62.0 + - - +
625J THR 3.2 2.7 - - - -
626J TYR* 2.9 53.2 + + - +
627J GLY 3.2 8.5 + - - -
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Residues in contact with ALA 624 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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612J GLN* 4.4 7.4 - - - +
620J ALA 3.6 4.8 + - - +
621J LEU* 3.0 22.5 + - + +
623J PHE* 1.3 76.0 - - - +
625J THR* 1.3 53.4 - - + +
627J GLY* 3.1 2.6 + - - -
628J GLY* 2.8 31.5 + - - -
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Residues in contact with THR 625 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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436J MLY 6.3 0.2 - - + -
621J LEU 5.3 0.4 - - - +
622J LEU 4.1 18.8 - - - +
623J PHE 4.3 0.2 - - - -
624J ALA* 1.3 73.9 - - + +
626J TYR* 1.3 75.0 + - + +
628J GLY* 3.8 1.6 + - - +
629J GLU* 3.5 35.5 + - - +
644J SER* 4.0 0.5 + - - -
646J PHE* 4.9 12.1 - - - -
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Residues in contact with TYR 626 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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436J MLY 0.8 128.1 + - + -
603J LEU* 4.5 8.7 - - + -
605J GLU* 6.5 0.4 - - + -
608J ILE* 4.5 17.3 - - + -
612J GLN* 3.6 2.5 - - - +
622J LEU 4.0 5.8 - - - -
623J PHE* 2.9 40.6 + + - +
625J THR* 1.3 86.9 - - + +
627J GLY* 1.3 63.6 + - - +
629J GLU* 3.5 12.6 + - - +
630J ALA* 3.6 12.0 + - - +
645J SER* 5.8 3.0 - - - -
646J PHE* 5.2 15.5 - + - -
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Residues in contact with GLY 627 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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612J GLN* 2.3 40.3 - - - +
624J ALA 3.1 4.0 + - - -
626J TYR* 1.3 75.5 - - - +
628J GLY* 1.4 59.3 + - - +
630J ALA* 4.0 14.2 + - - +
631J GLU* 5.2 3.8 + - - +
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Residues in contact with GLY 628 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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624J ALA 2.8 17.9 + - - -
625J THR* 3.8 3.1 + - - -
626J TYR 3.2 0.6 - - - -
627J GLY* 1.4 74.6 - - - +
629J GLU* 1.4 57.3 + - - +
630J ALA 3.5 0.2 - - - -
631J GLU* 4.3 19.6 - - - +
643J GLY* 3.0 6.8 - - - +
644J SER* 3.5 3.6 + - - -
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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