Contacts of the helix formed by residues 385 - 389 (chain C) in PDB entry 1JLH
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 ASN 385 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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342C GLN* 3.0 28.9 + - - +
381C GLU* 4.4 11.5 + - + +
382C PRO* 3.4 16.8 - - - +
383C GLY 3.2 2.2 - - - -
384C THR* 1.3 77.2 + - - +
386C GLY* 1.3 62.4 + - - +
388C HIS* 3.1 13.2 + - - +
389C ALA* 3.4 13.5 + - - +
157D GLY* 5.7 0.3 + - - -
160D ASP* 6.1 0.4 - - - +
161D LEU* 5.6 8.2 - - + +
184D SER* 3.2 26.4 + - - +
185D ASN* 3.3 25.3 + - - +
190D HIS* 4.9 1.2 - - - -
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Residues in contact with GLY 386 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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381C GLU* 3.7 25.0 - - - +
382C PRO 2.9 13.9 + - - -
383C GLY* 5.9 0.2 - - - -
385C ASN* 1.3 75.6 - - - +
387C GLN* 1.3 57.1 + - - +
389C ALA* 2.9 17.7 + - - -
390C PHE* 3.0 27.2 + - - -
391C TYR* 3.2 13.8 - - - -
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Residues in contact with GLN 387 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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340C TYR* 2.7 40.5 + - - +
383C GLY* 5.7 0.2 - - - -
384C THR* 3.2 23.3 - - - +
386C GLY* 1.3 75.6 - - - +
388C HIS* 1.3 75.2 + - + +
389C ALA 3.6 0.5 + - - -
391C TYR* 3.2 42.7 + - + +
392C GLN 5.3 0.2 + - - -
427C ASN* 2.8 29.4 - - - +
431C GLN* 3.5 29.5 + - - +
216D GLU* 4.6 0.2 - - - +
357D GLU* 5.5 0.7 - - - +
514D VAL* 5.6 5.7 - - - +
518D LYS* 6.1 0.3 - - - -
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Residues in contact with HIS 388 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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384C THR* 2.9 39.5 + - - +
385C ASN* 3.1 6.9 + - - +
387C GLN* 1.3 92.3 + - + +
389C ALA* 1.3 58.3 + - - +
156D ILE* 3.8 29.9 - - + +
157D GLY* 3.4 34.4 - - - +
184D SER 5.5 0.2 - - - -
216D GLU* 3.1 38.1 + - - +
353D GLN* 3.5 7.6 - - - +
357D GLU* 4.0 9.8 - - - +
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Residues in contact with ALA 389 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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381C GLU* 6.0 2.2 - - + -
385C ASN 3.6 12.8 - - - +
386C GLY* 2.9 7.9 + - - +
387C GLN 3.3 1.0 + - - -
388C HIS* 1.3 80.7 - - - +
390C PHE* 1.3 70.1 + - + +
391C TYR 3.9 0.4 - - - -
161D LEU* 5.2 10.3 - - + -
349D ALA 5.4 3.4 - - - +
352D GLN* 5.6 0.9 - - + +
353D GLN* 3.2 47.5 - - + +
357D GLU* 3.5 14.7 - - - +
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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