Contacts of the helix formed by residues 555 - 562 (chain I) in PDB entry 4K4I
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 THR 555 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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500I ALA* 3.6 12.3 - - - +
553I THR 3.0 1.4 + - - +
554I PRO* 1.3 86.8 - - + +
556I GLU* 1.3 66.2 + - - +
557I LYS* 3.5 19.4 + - + +
558I ASP* 2.4 48.8 + - - +
559I VAL* 3.5 4.5 + - - +
605I ACT 3.5 22.4 - - + +
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Residues in contact with GLU 556 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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419I ARG* 3.0 33.5 + - - -
500I ALA* 3.8 20.5 - - - +
503I LEU* 3.5 6.5 - - + +
504I LEU* 3.4 22.3 + - + -
555I THR* 1.3 70.7 - - - +
557I LYS* 1.3 55.0 + - - +
559I VAL* 2.8 30.6 + - - +
560I PHE* 3.2 17.7 + - + -
567I TYR* 3.7 14.7 + - + -
573I ARG* 2.8 43.1 + - - +
605I ACT 2.7 20.6 + - - +
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Residues in contact with LYS 557 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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555I THR* 3.2 14.4 + - + +
556I GLU* 1.3 77.0 - - - +
558I ASP* 1.3 58.8 + - - +
560I PHE* 3.2 5.8 + - - +
561I ARG* 2.9 29.0 + - - +
567I TYR* 3.4 53.0 - - + +
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Residues in contact with ASP 558 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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552I PRO 5.1 1.3 - - - +
553I THR* 4.2 16.8 - - + -
554I PRO* 4.0 13.1 - - - +
555I THR* 2.4 43.3 + - - +
557I LYS* 1.3 74.7 - - - +
559I VAL* 1.3 66.1 + - - +
561I ARG* 2.7 36.6 + - - +
562I LEU* 2.9 30.5 + - + +
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Residues in contact with VAL 559 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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500I ALA* 4.8 2.7 - - + -
501I CYS* 3.9 18.4 - - - -
504I LEU* 3.5 28.7 - - + -
516I MET* 4.5 3.1 - - + -
527I LEU* 3.9 18.6 - - + -
532I LEU* 4.3 7.1 - - + +
553I THR* 3.7 30.1 - - + -
555I THR 4.1 3.8 - - - +
556I GLU* 2.8 18.4 + - - +
558I ASP* 1.3 74.6 - - - +
560I PHE* 1.3 63.1 + - - +
562I LEU* 3.3 8.8 + - - +
563I LEU* 3.4 27.9 + - + +
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Residues in contact with PHE 560 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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504I LEU* 4.0 13.0 - - + -
512I PHE* 3.6 38.1 - + - -
516I MET* 4.0 13.0 - - + -
556I GLU 3.2 20.1 + - - -
557I LYS 3.2 6.8 + - - +
559I VAL* 1.3 76.6 - - + +
561I ARG* 1.3 60.0 - - - +
563I LEU* 3.3 9.7 + - - -
565I LEU* 2.8 56.7 + - + +
566I PRO 3.5 12.8 - - - -
567I TYR* 3.7 25.4 - + - +
568I ARG* 3.7 23.1 - - + -
573I ARG* 3.9 26.2 - - - -
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Residues in contact with ARG 561 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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557I LYS 2.9 16.2 + - - +
558I ASP* 2.7 42.4 + - - +
560I PHE* 1.3 72.1 - - - +
562I LEU* 1.3 84.5 + - - +
563I LEU 3.0 4.0 - - - -
564I GLY* 2.8 22.0 + - - -
565I LEU 4.1 6.1 - - - +
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Residues in contact with LEU 562 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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523I LYS* 4.7 2.4 + - - +
525I MET* 3.5 19.3 - - - +
532I LEU* 3.8 28.0 - - + -
551I LEU* 4.0 27.1 - - + -
552I PRO 4.5 4.5 - - - +
553I THR* 3.9 18.4 - - + -
558I ASP* 2.9 23.1 + - + +
559I VAL 3.3 0.8 + - - +
561I ARG* 1.3 96.6 - - - +
563I LEU* 1.3 58.4 + - - +
564I GLY 3.4 0.2 - - - -
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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