Contacts of the helix formed by residues 288 - 293 (chain G) in PDB entry 5JLH
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 LYS 288 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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286G LEU* 3.4 24.9 + - + +
287G GLU* 1.3 70.2 - - - +
289G SER* 1.3 69.0 + - - +
290G ARG 3.1 3.4 + - - -
291G ALA* 3.2 19.4 + - - +
301G PHE* 5.1 1.6 - - - -
445G LYS* 3.7 50.0 - - + +
446G ALA 4.3 8.1 - - - +
448G TYR* 5.2 5.1 - - + -
449G GLU* 3.9 21.0 + - + +
616G ASP* 3.2 26.2 + - - -
668G ARG* 3.5 14.3 - - - +
670G VAL* 4.6 8.5 - - + -
673G LEU* 3.4 23.4 - - - +
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Residues in contact with SER 289 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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287G GLU* 4.3 6.4 - - - +
288G LYS* 1.3 79.1 + - - +
290G ARG* 1.3 58.8 + - - +
291G ALA 3.2 0.2 - - - -
292G ILE* 3.1 14.7 - - - +
293G ARG* 2.9 31.5 + - - +
445G LYS* 4.1 17.5 - - - +
491G GLU* 2.9 37.5 + - - +
613G LYS* 4.9 8.5 - - - -
670G VAL* 5.3 6.3 - - - -
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Residues in contact with ARG 290 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251G ALA* 3.7 26.0 - - - -
253G THR* 4.2 5.2 - - - +
261G ARG* 3.1 39.8 - - - +
287G GLU* 3.0 35.4 + - - +
288G LYS 3.1 0.8 - - - -
289G SER* 1.3 81.5 + - - +
291G ALA* 1.3 50.6 + - - +
293G ARG 2.8 11.9 - - - +
294G GLN* 2.7 35.3 + - + +
295G ALA* 5.0 7.7 - - - +
298G GLU* 3.2 25.6 + - - +
299G CYS 4.4 5.0 + - - -
300G SER* 4.3 11.8 - - - +
301G PHE* 3.9 24.9 - - + -
483G GLU* 5.3 1.2 + - - -
485G PHE* 5.7 4.6 - - - -
491G GLU* 4.9 10.4 + - - +
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Residues in contact with ALA 291 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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288G LYS 3.2 12.7 + - - +
289G SER 3.2 0.8 - - - -
290G ARG* 1.3 78.8 - - - +
292G ILE* 1.3 58.3 + - - +
294G GLN* 2.8 16.8 + - - +
300G SER* 5.0 0.6 - - - -
301G PHE* 4.1 12.5 - - + -
304G PHE* 4.1 32.9 - - + -
329G PHE* 3.8 12.8 - - - +
330G LEU* 5.4 2.3 - - - +
372G VAL* 5.2 8.5 - - + -
373G LEU* 5.7 1.9 - - - +
444G ALA* 6.3 0.4 - - + -
445G LYS* 5.5 3.6 - - + -
448G TYR* 4.8 13.2 - - + -
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Residues in contact with ILE 292 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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288G LYS 4.1 0.4 + - - -
289G SER* 3.1 22.4 - - - +
291G ALA* 1.3 78.4 - - - +
293G ARG* 1.3 79.2 + - + +
294G GLN* 3.5 2.8 - - - +
328G ARG* 4.5 1.8 - - - +
329G PHE* 3.2 69.6 - - + +
441G GLU* 3.7 30.3 - - + +
444G ALA* 5.7 0.2 - - + -
445G LYS* 3.5 37.6 - - + +
613G LYS* 6.5 0.2 - - - -
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Residues in contact with ARG 293 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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289G SER* 2.9 18.0 + - - +
290G ARG* 2.8 19.9 - - - +
291G ALA 3.4 0.6 - - - -
292G ILE* 1.3 98.8 - - + +
294G GLN* 1.3 66.2 + - - +
328G ARG* 5.1 9.6 - - - +
438G PHE* 5.9 0.8 - - - -
441G GLU* 4.6 20.0 + - - -
491G GLU* 5.1 5.5 - - - +
609G GLU* 5.8 7.7 - - - +
612G MET* 3.8 40.1 + - - +
613G LYS* 4.5 33.5 - - + +
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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