Contacts of the helix formed by residues 367 - 373 (chain B) 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 SER 367 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116B GLU* 4.2 17.5 - - - -
364B SER 4.1 10.7 + - - -
365B GLY* 5.2 0.2 - - - -
366B PRO* 1.3 73.5 - - - +
368B ILE* 1.3 60.8 + - - +
369B VAL* 2.8 13.4 + - - -
370B HIS* 3.5 18.7 + - - +
371B ARG* 4.3 2.4 + - - +
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Residues in contact with ILE 368 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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356B ILE* 3.3 40.6 - - + -
360B GLU* 5.2 4.0 - - + -
361B TYR* 4.7 12.3 - - + +
364B SER* 3.2 42.6 - - - +
365B GLY 3.2 13.5 - - - +
366B PRO* 3.0 3.8 - - + +
367B SER* 1.3 78.5 - - - +
369B VAL* 1.3 67.8 - - + +
370B HIS 3.2 0.9 - - - -
371B ARG* 3.5 30.9 - - - +
372B LYS* 3.3 29.4 + - + +
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Residues in contact with VAL 369 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115B ARG* 3.7 26.7 - - + +
116B GLU* 4.2 3.6 - - + -
119B THR* 3.2 32.8 - - + +
133B VAL* 3.4 33.9 - - + -
356B ILE* 4.5 10.5 - - + -
366B PRO 3.2 18.1 + - - +
367B SER 2.8 2.0 + - - +
368B ILE* 1.3 79.4 - - + +
370B HIS* 1.3 63.5 + - + +
372B LYS* 4.4 0.3 - - - +
373B CYS* 3.0 38.4 + - - -
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Residues in contact with HIS 370 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112B LYS* 3.1 61.4 + - + +
115B ARG* 3.8 33.9 + - + +
116B GLU* 3.2 32.8 + - + +
367B SER 3.5 8.9 + - - +
368B ILE 3.2 0.4 - - - -
369B VAL* 1.3 74.8 - - - +
371B ARG* 1.3 64.4 + - - +
373B CYS* 2.8 20.9 - - - +
374B PHE 5.8 1.8 + - - -
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Residues in contact with ARG 371 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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364B SER* 4.1 14.4 + - - -
367B SER 4.3 1.7 + - - +
368B ILE* 3.5 40.7 - - - +
370B HIS* 1.3 80.7 - - - +
372B LYS* 1.3 63.0 + - + +
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Residues in contact with LYS 372 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132B TYR* 5.8 0.9 - - + -
353B GLN 5.7 2.6 + - - -
354B MET* 3.8 24.6 - - + +
355B TRP 4.1 4.3 + - - +
356B ILE* 4.0 20.2 - - + +
360B GLU* 3.3 34.9 + - - -
368B ILE* 3.3 20.9 + - + +
369B VAL 4.4 0.4 - - - +
370B HIS 3.3 0.6 - - - -
371B ARG* 1.3 84.8 - - + +
373B CYS* 1.3 64.0 + - + +
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Residues in contact with CYS 373 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115B ARG* 5.0 0.9 - - - -
132B TYR* 3.3 37.2 - - + +
133B VAL* 3.6 35.0 - - - -
356B ILE* 4.6 5.6 - - + -
369B VAL* 3.0 33.3 + - - +
370B HIS* 2.8 22.7 - - - +
372B LYS* 1.3 80.6 - - + +
374B PHE* 1.3 67.2 + - - +
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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