Contacts of the helix formed by residues 611 - 620 (chain A) in PDB entry 3IAY
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 611 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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610A ASN* 1.3 75.2 - - - +
612A LEU* 1.3 66.5 + - - +
613A TYR 3.6 1.3 - - - -
614A PRO* 3.4 8.8 - - - +
615A SER* 3.0 19.1 + - - -
671A ILE* 4.2 35.1 - - - +
674A ARG* 3.4 18.9 + - - +
986A DCP 2.8 33.0 + - - -
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Residues in contact with LEU 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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609A PHE* 3.6 21.5 - - + -
610A ASN 3.1 4.9 + - - -
611A SER* 1.3 71.3 - - - +
613A TYR* 1.3 89.5 + - + +
615A SER* 2.7 22.9 + - - +
616A ILE* 2.9 21.0 + - + +
731A GLY* 4.4 8.5 - - - +
734A MET* 3.6 32.3 - - + -
763A THR* 4.2 9.6 - - + +
764A ASP* 3.4 36.6 - - + +
986A DCP 2.9 18.3 + - - +
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Residues in contact with TYR 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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590A ALA* 3.9 14.0 + - - +
612A LEU* 1.3 99.2 - - + +
614A PRO* 1.3 69.4 - - + +
616A ILE* 3.2 7.7 + - + +
617A MET* 3.1 27.5 + - - +
705A ASN* 4.5 0.2 - - - +
708A TYR* 3.5 46.4 - + + -
727A VAL* 3.4 28.1 - - + +
728A THR* 3.8 22.9 + - + +
731A GLY* 4.9 4.7 - - - -
763A THR* 3.8 23.2 - - + +
986A DCP 2.9 40.6 + - + +
5T G 5.1 5.6 + - - -
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Residues in contact with PRO 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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611A SER* 3.4 17.0 - - - +
613A TYR* 1.3 92.3 - - + +
615A SER* 1.3 55.0 + - - +
617A MET* 3.2 4.1 + - + +
618A MET* 2.9 36.1 + - + +
667A LEU* 3.9 24.9 - - + -
671A ILE* 3.7 22.4 - - + -
704A ALA* 4.1 22.0 - - + +
705A ASN* 3.3 26.0 - - - +
708A TYR* 5.7 0.7 - - + -
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Residues in contact with SER 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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609A PHE* 5.6 0.2 - - - +
610A ASN 4.0 8.1 + - - -
611A SER* 3.0 14.4 + - - -
612A LEU* 2.7 28.0 + - - +
614A PRO* 1.3 76.3 - - - +
616A ILE* 1.3 57.9 + - - +
618A MET* 3.2 15.4 - - - +
619A ALA* 2.8 32.6 + - - +
796A PRO* 4.0 9.3 - - - +
797A ILE* 3.6 32.0 - - - +
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Residues in contact with ILE 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 LEU* 2.9 35.0 + - + +
613A TYR* 3.4 13.9 - - + +
615A SER* 1.3 79.5 + - - +
617A MET* 1.3 61.4 + - - +
619A ALA* 4.5 1.3 - - - -
620A HIS* 3.0 31.9 + - + +
622A LEU* 4.1 8.9 - - + +
727A VAL* 3.7 25.1 - - + +
730A TYR* 3.7 31.4 - - + -
731A GLY* 3.8 11.0 - - - +
734A MET* 3.6 33.2 - - + -
797A ILE* 4.8 2.0 - - + -
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Residues in contact with MET 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 TYR 3.1 14.5 + - - +
614A PRO* 3.7 2.0 - - - +
616A ILE* 1.3 74.6 - - - +
618A MET* 1.3 57.8 + - - +
621A ASN* 3.1 7.3 + - - -
622A LEU* 3.0 42.5 + - + +
663A LEU* 3.5 39.3 - - + -
664A PRO* 3.7 6.0 - - + +
667A LEU* 3.6 26.9 - - + -
707A VAL* 4.3 8.1 - - + -
708A TYR* 3.9 32.3 - - - -
711A THR* 4.7 0.4 - - + -
723A ILE* 4.0 14.1 - - + -
727A VAL* 3.5 21.8 - - + -
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Residues in contact with MET 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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614A PRO* 2.9 38.1 + - + +
615A SER* 3.2 17.3 - - - +
617A MET* 1.3 75.7 - - - +
619A ALA* 1.3 66.4 + - - +
620A HIS 3.2 0.7 + - - -
621A ASN* 3.3 10.0 + - - +
664A PRO* 3.9 32.4 - - + +
667A LEU* 4.1 12.6 - - + -
668A ASP* 4.2 16.6 - - - +
671A ILE* 3.4 29.4 - - + -
794A LYS* 4.8 1.2 + - - -
796A PRO* 4.0 24.0 - - + -
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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 SER 2.8 22.9 + - - +
616A ILE 3.4 2.9 + - - +
618A MET* 1.3 74.3 - - - +
620A HIS* 1.3 65.9 + - + +
621A ASN* 3.7 1.2 + - - +
794A LYS* 2.6 41.9 + - + +
795A HIS 3.5 24.5 - - - +
796A PRO* 3.8 0.6 - - - +
797A ILE* 3.8 24.5 - - + -
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Residues in contact with HIS 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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616A ILE* 3.0 28.5 + - + +
617A MET 3.9 0.2 - - - -
619A ALA* 1.3 94.1 + - + +
621A ASN* 1.3 70.6 + - - +
622A LEU* 3.2 23.5 + - + +
645A VAL* 5.3 10.6 - - + +
653A PHE* 4.6 5.4 - - - +
654A VAL 4.8 0.5 - - - +
730A TYR* 3.5 55.7 + + + +
734A MET* 5.5 2.0 - - - -
794A LYS* 4.5 17.6 - - + +
797A ILE* 4.3 9.4 - - + +
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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