Contacts of the helix formed by residues 615 - 619 (chain A) in PDB entry 4KSP
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 615 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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575A ASP* 4.0 10.4 + - - +
577A LYS* 2.7 42.7 + - - +
614A GLY* 1.3 69.0 + - - -
616A ILE* 1.3 65.5 + - - +
617A LEU 3.4 2.7 + - - -
618A TRP* 3.5 28.9 + - - +
619A MET* 4.0 14.7 + - - +
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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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614A GLY* 3.7 11.9 + - - +
615A SER* 1.3 71.7 - - - +
617A LEU* 1.3 75.2 + - + +
618A TRP* 3.1 3.3 - - - -
619A MET* 3.0 45.3 + - + +
624A ILE* 4.3 10.0 - - + +
655A TYR* 5.8 0.3 - - - -
661A ARG* 3.5 42.1 - - + +
664A ILE* 4.0 28.7 - - + -
665A ILE* 3.8 28.3 - - + -
668A VAL* 6.1 0.7 - - - +
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Residues in contact with LEU 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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615A SER 3.4 1.2 - - - -
616A ILE* 1.3 89.0 - - + +
618A TRP* 1.3 83.1 + - + +
619A MET 3.6 1.0 + - - +
639A TYR* 4.5 2.8 + - - -
643A ILE* 3.4 23.7 - - - +
653A LEU* 4.2 35.4 - - + -
654A PRO* 3.9 23.3 - - + +
655A TYR* 3.8 34.4 - - + +
664A ILE* 4.8 9.9 - - + -
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Residues in contact with TRP 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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537A TYR* 5.1 8.7 - + - -
576A LEU 3.8 12.1 - - - +
577A LYS* 3.4 38.2 - - + +
578A SER* 3.9 8.1 - - - -
579A ASN* 5.9 0.4 - - + -
615A SER* 3.5 32.7 + - - +
616A ILE 3.1 1.2 - - - -
617A LEU* 1.3 102.2 - - + +
619A MET* 1.3 58.8 + - - +
620A ALA 3.8 0.3 + - - -
636A SER 5.0 0.7 - - - +
639A TYR* 3.6 6.7 - - - -
640A ALA* 3.5 35.1 + - + +
643A ILE* 3.5 28.0 - - + +
644A VAL* 4.1 1.3 - - + +
647A GLU* 2.8 41.1 + - - -
653A LEU* 4.0 17.7 - - + -
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Residues in contact with MET 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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614A GLY* 6.0 0.4 - - - -
615A SER 4.0 11.4 + - - +
616A ILE* 3.0 42.3 + - + +
617A LEU 3.3 0.9 - - - +
618A TRP* 1.3 77.1 - - - +
620A ALA* 1.3 63.9 + - - +
621A PRO 3.9 0.3 - - - -
623A VAL* 3.5 35.0 - - + +
624A ILE* 3.8 42.7 - - + +
626A MET* 5.2 5.6 - - + -
632A TYR* 5.2 5.2 - - + +
639A TYR* 3.5 10.8 + - - -
668A VAL* 4.2 5.2 - - - +
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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