Contacts of the helix formed by residues 585 - 599 (chain V) in PDB entry 5IY6
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 SER 585 (chain V).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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583V PRO 3.6 4.7 + - - -
584V THR* 1.3 74.4 - - - +
586V GLN* 1.3 59.8 + - - +
587V GLY* 3.7 3.5 + - - -
588V GLU* 3.2 25.1 + - - +
589V ARG* 2.8 32.8 + - - +
51X C 5.5 7.6 - - - -
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Residues in contact with GLN 586 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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585V SER* 1.3 73.7 - - - +
587V GLY* 1.3 59.5 + - - +
589V ARG* 3.2 15.1 + - - +
590V MET* 2.7 35.0 + - - +
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Residues in contact with GLY 587 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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585V SER* 3.4 4.5 + - - -
586V GLN* 1.3 76.8 - - - +
588V GLU* 1.4 58.2 + - - +
590V MET* 3.5 4.9 + - - +
591V GLN* 3.1 27.8 + - - +
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Residues in contact with GLU 588 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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584V THR* 3.7 17.5 + - + +
585V SER* 3.2 19.2 + - - +
587V GLY* 1.4 72.9 - - - +
589V ARG* 1.4 64.3 + - - +
591V GLN* 3.5 12.0 + - + +
592V ILE* 3.0 42.5 + - + +
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Residues in contact with ARG 589 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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580V ILE* 4.1 30.3 - - + +
581V TYR 3.4 9.1 + - - -
582V GLY* 2.8 34.6 + - - -
584V THR* 3.0 28.9 + - + +
585V SER 2.8 28.3 + - - +
586V GLN* 3.6 13.7 - - - +
588V GLU* 1.4 71.3 - - - +
590V MET* 1.4 57.8 + - - +
592V ILE* 3.3 1.8 + - - +
593V LEU* 2.9 42.0 + - + +
610V VAL* 4.6 17.6 + - - +
615V PHE* 5.2 14.6 - - - -
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Residues in contact with MET 590 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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586V GLN 2.7 21.1 + - - +
587V GLY* 4.0 4.9 - - - +
589V ARG* 1.4 68.3 - - - +
591V GLN* 1.3 59.5 + - - +
593V LEU* 4.5 9.2 - - + -
594V GLN* 2.9 62.4 + - - +
597V LYS* 6.2 3.4 - - - +
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Residues in contact with GLN 591 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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587V GLY 3.1 14.9 + - - +
588V GLU* 3.5 16.0 + - - +
590V MET* 1.3 74.5 - - - +
592V ILE* 1.3 60.1 + - + +
594V GLN* 3.9 4.3 - - - +
595V ASN* 3.0 47.7 + - - +
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Residues in contact with ILE 592 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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578V PRO* 3.6 35.4 - - + -
579V TYR 4.2 17.5 - - - +
580V ILE* 4.3 19.7 - - + -
584V THR* 4.7 1.8 - - + -
588V GLU* 3.0 47.3 + - + +
589V ARG 3.9 3.1 - - - +
591V GLN* 1.3 77.4 - - + +
593V LEU* 1.3 53.1 + - - +
595V ASN* 3.5 6.5 + - - +
596V PHE* 2.8 32.6 + - - +
602V ILE* 4.9 1.8 - - + +
605V ILE* 3.8 17.3 - - + -
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Residues in contact with LEU 593 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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580V ILE* 3.7 22.4 - - + -
589V ARG* 2.9 30.5 + - + +
590V MET* 4.0 9.4 - - + +
592V ILE* 1.3 74.0 - - - +
594V GLN* 1.4 57.4 + - - +
596V PHE* 3.4 5.1 + - - +
597V LYS* 3.0 49.0 + - - +
605V ILE* 4.2 8.5 - - + -
607V ILE* 5.3 0.9 - - + -
615V PHE* 4.6 21.3 - - + -
616V ASP* 5.2 8.1 - - - +
618V PRO* 3.6 37.9 - - + -
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Residues in contact with GLN 594 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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590V MET* 2.9 50.1 + - - +
591V GLN* 4.0 4.8 - - - +
593V LEU* 1.4 67.9 - - - +
595V ASN* 1.3 61.6 + - - +
597V LYS* 4.2 7.6 - - - +
598V HIS* 2.9 56.1 + - + +
599V ASN 4.0 0.2 + - - -
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Residues in contact with ASN 595 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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591V GLN* 3.0 38.5 + - - +
592V ILE* 3.6 7.0 - - - +
594V GLN* 1.3 78.4 - - - +
596V PHE* 1.3 59.0 + - - +
599V ASN* 2.8 65.5 + - - +
602V ILE* 3.8 19.6 - - + +
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Residues in contact with PHE 596 (chain V).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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557V LYS* 2.9 48.4 + - + +
558V ILE 3.3 40.4 - - - -
559V ILE* 3.7 18.8 - - + -
592V ILE 2.8 20.6 + - - +
593V LEU* 3.6 6.7 - - - +
595V ASN* 1.3 71.3 - - - +
597V LYS* 1.4 55.8 + - - +
602V ILE* 3.2 19.2 - - + +
603V ASN* 3.4 22.9 - - - -
604V THR 3.9 0.2 - - - -
605V ILE* 3.8 28.5 - - + -
618V PRO* 3.7 22.9 - - + -
619V GLU 3.7 18.4 - - - -
620V ALA* 4.0 1.6 - - + -
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Residues in contact with LYS 597 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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557V LYS* 4.5 8.2 - - - +
590V MET* 6.2 3.6 - - - +
593V LEU* 3.0 41.3 + - - +
594V GLN* 4.2 6.3 - - - +
596V PHE* 1.4 76.4 - - - +
598V HIS* 1.3 78.9 + - + +
616V ASP* 5.2 10.3 + - - -
618V PRO* 3.8 31.1 - - + +
619V GLU* 4.7 12.8 - - + +
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Residues in contact with HIS 598 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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557V LYS* 4.9 0.9 - - - -
594V GLN* 2.9 46.6 + - + +
597V LYS* 1.3 91.6 - - + +
599V ASN* 1.3 62.8 + - - +
600V PRO* 3.2 14.7 - - - +
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Residues in contact with ASN 599 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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557V LYS* 3.0 17.1 + - - -
594V GLN 4.0 0.4 + - - -
595V ASN* 2.8 49.4 + - - +
598V HIS* 1.3 71.8 - - - +
600V PRO* 1.4 64.0 - - - +
601V LYS* 2.9 37.0 + - - +
602V ILE* 3.0 21.9 + - + +
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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