Contacts of the helix formed by residues 358 - 365 (chain A) 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 358 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123A PHE* 3.6 44.1 - - + -
124A GLU* 6.0 1.7 - - - +
127A ASN* 3.4 26.3 + - - +
128A THR 3.6 11.2 - - - +
129A PRO* 2.8 26.0 + - + +
356A ILE 3.9 0.6 + - - -
357A SER* 1.3 72.4 - - - +
359A GLN* 1.3 63.4 + - - +
361A TYR* 3.3 4.7 + - + +
362A ASP* 2.9 58.1 + - - +
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Residues in contact with GLN 359 (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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357A SER* 3.1 9.0 - - - -
358A LYS* 1.3 77.6 - - - +
360A GLU* 1.3 64.2 + - + +
362A ASP* 3.0 20.6 + - - +
363A GLU* 2.6 46.6 + - - +
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Residues in contact with GLU 360 (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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355A TRP 3.8 3.9 - - - +
356A ILE* 4.2 3.1 - - + -
357A SER* 3.2 34.8 + - - +
359A GLN* 1.3 80.8 - - + +
361A TYR* 1.3 57.1 + - - +
363A GLU* 3.3 8.8 + - - +
364A SER* 2.9 38.6 + - - +
368A ILE* 5.2 6.1 - - + -
372A LYS* 3.3 34.7 + - - -
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Residues in contact with TYR 361 (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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119A THR* 5.2 1.1 - - - -
120A GLN* 4.1 13.2 - - - +
123A PHE* 3.2 58.6 - + + -
124A GLU* 3.5 32.8 + - + +
356A ILE* 4.8 3.6 - - + +
357A SER 3.0 8.7 + - - +
358A LYS* 3.4 7.6 - - + +
359A GLN 3.3 0.2 - - - -
360A GLU* 1.3 77.4 - - - +
362A ASP* 1.3 75.1 + - - +
365A GLY* 2.7 48.8 + - - -
366A PRO* 3.2 43.4 - - + +
368A ILE* 4.7 5.2 - - + -
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Residues in contact with ASP 362 (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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358A LYS* 2.9 57.7 + - - +
359A GLN* 3.0 9.9 + - - +
361A TYR* 1.3 90.2 - - - +
363A GLU* 1.3 63.5 + - + +
365A GLY* 4.5 1.0 + - - -
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Residues in contact with GLU 363 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
359A GLN* 2.6 60.6 + - - +
360A GLU* 3.3 10.8 - - - +
362A ASP* 1.3 81.1 - - + +
364A SER* 1.3 66.5 + - - +
365A GLY 3.8 0.2 + - - -
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Residues in contact with SER 364 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
360A GLU* 2.9 21.3 + - - +
363A GLU* 1.3 79.0 - - - +
365A GLY* 1.3 60.5 + - - +
367A SER* 4.1 7.8 + - - -
368A ILE* 3.2 28.7 - - - +
371A ARG* 4.1 15.3 + - - -
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Residues in contact with GLY 365 (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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361A TYR* 2.7 29.4 + - - +
362A ASP 4.5 1.1 + - - -
363A GLU 3.6 2.0 + - - -
364A SER* 1.3 71.9 - - - +
366A PRO* 1.3 75.3 - - - +
367A SER 3.3 3.7 + - - -
368A ILE* 3.2 22.2 - - - +
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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