Contacts of the helix formed by residues 616 - 628 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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350D ALA* 4.5 24.0 - - + -
353D MLY 3.7 23.8 - - + -
354D LEU* 5.0 5.8 - - + -
389D LEU 4.4 4.5 - - - +
390D MET 3.4 33.0 - - - +
391D GLY* 3.6 6.7 - - - +
614D SER* 3.0 3.8 + - - +
615D SER* 1.3 80.6 - - - +
617D MLY 1.3 54.5 + - - +
618D THR 4.7 0.9 - - - +
619D LEU* 2.7 39.0 + - + +
620D ALA 3.0 8.4 + - - -
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Residues in contact with MLY 617 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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346D ASP* 5.4 10.3 - - - +
614D SER 5.0 1.6 - - - +
615D SER 3.5 8.0 + - - +
616D VAL* 1.3 71.3 + - - +
618D THR* 1.3 53.2 + - - +
620D ALA* 2.9 11.8 + - - +
621D LEU* 2.6 48.4 + - + +
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Residues in contact with THR 618 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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346D ASP* 5.1 4.5 + - - -
347D GLU* 4.0 18.2 + - - +
350D ALA* 3.7 29.3 - - + +
354D LEU* 4.4 7.4 - - + -
437D MET* 6.3 0.2 - - + -
440D TRP* 3.6 35.6 - - + -
616D VAL* 3.2 2.4 - - - -
617D MLY 1.3 79.7 + - - +
619D LEU* 1.3 61.9 + - - +
621D LEU* 2.9 14.4 + - - +
622D LEU* 2.8 31.4 + - + +
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Residues in contact with LEU 619 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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354D LEU* 4.6 13.4 - - + +
390D MET* 3.6 41.3 - - + +
392D LEU* 4.8 0.9 - - + -
433D VAL* 4.5 11.4 - - + -
611D TYR* 3.9 28.8 - - + +
614D SER* 4.0 9.2 - - - +
616D VAL* 2.7 22.9 + - + +
618D THR* 1.3 77.9 - - - +
620D ALA* 1.3 66.4 + - - +
622D LEU* 3.5 29.7 + - + +
623D PHE* 3.7 24.7 + - + +
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Residues in contact with ALA 620 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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611D TYR 3.5 19.9 + - - +
612D GLN* 4.2 15.2 - - - +
614D SER* 4.4 11.6 - - - +
616D VAL 3.0 6.3 + - - +
617D MLY 2.9 21.0 + - - +
619D LEU* 1.3 79.1 - - - +
621D LEU* 1.3 66.7 + - + +
623D PHE* 3.2 12.8 + - - +
624D ALA* 3.6 7.6 + - - +
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Residues in contact with LEU 621 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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440D TRP* 5.2 14.4 - - + +
617D MLY 2.6 28.4 + - + +
618D THR* 2.9 12.9 + - - +
620D ALA* 1.3 78.1 - - + +
622D LEU* 1.3 58.9 + - + +
623D PHE 2.8 10.8 + - - -
624D ALA* 3.0 26.5 + - + +
625D THR* 5.3 0.7 - - - +
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Residues in contact with LEU 622 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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354D LEU* 4.9 7.9 - - + -
433D VAL* 4.3 11.9 - - + +
436D MLY 3.5 34.4 - - + +
437D MET* 4.0 28.5 - - + +
440D TRP* 4.2 22.9 - - + -
618D THR* 2.8 36.6 - - + +
619D LEU* 3.7 26.7 - - + +
621D LEU* 1.3 79.8 - - + +
623D PHE* 1.5 56.7 + - + +
625D THR* 4.1 9.0 - - - +
626D TYR* 4.0 5.5 - - - -
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Residues in contact with PHE 623 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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429D LEU* 5.4 0.7 - - + -
432D ALA* 4.2 7.6 - - + -
433D VAL* 3.8 40.2 - - + -
436D MLY 4.0 13.2 - - + -
603D LEU* 4.6 0.7 - - + -
608D ILE* 3.7 37.0 - - + -
611D TYR* 3.2 38.6 - + + -
612D GLN* 3.2 18.6 + - + +
619D LEU* 3.7 13.2 + - + +
620D ALA 3.2 8.2 + - - +
621D LEU 2.8 6.9 + - - -
622D LEU* 1.5 70.3 - - + +
624D ALA* 1.3 62.5 + - - +
625D THR 3.2 2.5 - - - -
626D TYR* 2.9 54.2 + + - +
627D GLY 3.2 8.0 + - - -
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Residues in contact with ALA 624 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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612D GLN* 4.4 7.4 - - - +
620D ALA 3.6 5.7 + - - +
621D LEU* 3.0 23.3 + - + +
623D PHE* 1.3 75.9 - - - +
625D THR* 1.3 55.6 + - + +
627D GLY* 3.1 3.0 + - - -
628D GLY* 2.8 31.2 + - - -
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Residues in contact with THR 625 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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621D LEU 5.3 0.2 - - - +
622D LEU 4.1 19.1 - - - +
624D ALA* 1.3 73.7 - - + +
626D TYR* 1.3 75.1 + - + +
628D GLY* 4.3 2.1 - - - +
629D GLU* 3.5 35.9 + - - +
644D SER* 4.0 0.2 + - - -
646D PHE* 4.9 12.1 - - - -
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Residues in contact with TYR 626 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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436D MLY 0.8 128.5 + - + -
603D LEU* 4.5 8.7 - - + -
605D GLU* 6.5 0.9 - - + -
608D ILE* 4.5 17.0 - - + -
612D GLN* 4.3 2.9 - - - +
622D LEU 4.0 6.1 - - - -
623D PHE* 2.9 39.6 + + - +
625D THR* 1.3 87.1 - - + +
627D GLY* 1.3 62.6 + - - +
628D GLY 3.4 0.3 + - - -
629D GLU* 3.5 12.8 + - - +
630D ALA* 3.6 12.0 + - - +
645D SER* 5.8 3.0 - - - -
646D PHE* 5.2 15.0 - + - -
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Residues in contact with GLY 627 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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612D GLN* 2.3 39.2 - - - +
624D ALA 3.1 4.1 + - - -
626D TYR* 1.3 77.0 - - - +
628D GLY* 1.4 59.6 + - - +
629D GLU 3.8 0.2 + - - -
630D ALA* 4.0 14.2 + - - +
631D GLU* 5.2 3.5 + - - +
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Residues in contact with GLY 628 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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624D ALA 2.8 17.1 + - - -
625D THR* 3.8 3.5 + - - -
626D TYR 3.2 0.6 - - - -
627D GLY* 1.4 74.3 - - - +
629D GLU* 1.4 57.1 + - - +
630D ALA 3.5 0.2 - - - -
631D GLU* 4.3 19.2 - - - +
643D GLY* 3.0 6.5 - - - +
644D SER* 3.5 3.4 + - - -
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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