Contacts of the helix formed by residues 350 - 358 (chain A) in PDB entry 6J95
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 350 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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212A TYR* 4.4 0.4 - - - -
216A MET* 5.6 0.2 - - - -
257A LYS 3.9 5.2 - - - -
258A ALA* 3.3 13.7 - - - +
259A VAL 3.5 13.0 + - - -
261A ASN* 3.6 21.9 + - - +
348A ASP* 2.7 24.2 + - - -
349A PRO* 1.3 83.9 - - - +
351A ILE* 1.3 65.6 + - - +
352A LEU* 3.8 4.9 + - - +
353A HIS* 3.1 23.9 + - - +
354A PHE* 3.1 11.7 + - - +
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Residues in contact with ILE 351 (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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204A ILE* 4.8 3.6 - - + -
207A ALA* 3.9 23.3 - - + +
208A LEU* 4.3 14.8 - - + -
212A TYR* 3.3 37.7 - - + +
258A ALA 3.2 7.1 + - - +
259A VAL* 3.7 20.2 - - + +
349A PRO 3.8 0.2 + - - -
350A SER* 1.3 72.1 - - - +
352A LEU* 1.3 63.9 + - - +
354A PHE* 3.1 8.4 + - - +
355A LEU* 2.9 38.2 + - + +
371A LEU* 5.2 0.4 - - + -
374A MET* 4.0 33.9 - - + -
601A HEM 4.6 5.2 - - + -
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Residues in contact with LEU 352 (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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259A VAL 2.9 17.2 + - - +
260A PHE* 3.9 28.9 - - + +
261A ASN* 6.0 0.7 - - + -
324A LEU* 4.1 28.9 - - + +
325A ILE* 4.1 8.1 - - + -
328A CYS* 4.2 11.9 - - + -
350A SER* 3.2 2.4 - - - +
351A ILE* 1.3 77.5 - - - +
353A HIS* 1.3 61.7 + - - +
355A LEU* 3.4 4.4 + - - +
356A LEU* 3.0 32.6 + - + +
367A LEU* 3.7 32.8 - - + -
371A LEU* 4.0 21.9 - - + +
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Residues in contact with HIS 353 (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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328A CYS* 3.4 14.5 - - - -
331A MET* 3.6 27.6 - - + -
332A VAL* 3.8 15.7 - - + +
335A GLU* 2.9 28.5 + - - -
343A TYR* 3.0 22.3 + + - -
345A ASN* 3.5 13.6 - - + +
348A ASP* 2.6 46.3 + - + +
350A SER* 3.1 10.5 + - - +
352A LEU* 1.3 76.8 - - - +
354A PHE* 1.3 67.2 + - - +
356A LEU* 3.4 1.4 + - - +
357A ALA* 3.0 20.6 + - - +
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Residues in contact with PHE 354 (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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203A ALA 4.6 6.7 - - - -
206A PRO* 3.5 34.8 - - + -
207A ALA* 3.4 38.1 - - + +
209A HIS* 3.8 9.2 - + - -
212A TYR* 6.6 0.7 - - + -
339A PHE* 3.6 31.1 - + - -
341A GLU* 4.4 5.4 - - - -
343A TYR* 3.4 45.3 - + + -
344A MET* 6.3 0.2 - - - -
349A PRO 5.8 0.2 - - - +
350A SER 3.1 12.0 + - - +
351A ILE* 3.5 7.2 - - - +
353A HIS* 1.3 77.1 - - - +
355A LEU* 1.3 68.4 + - + +
357A ALA* 3.4 1.0 + - - +
358A SER* 3.0 25.9 + - - -
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Residues in contact with LEU 355 (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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200A ARG* 4.6 4.0 - - - +
203A ALA 3.5 25.1 - - - +
204A ILE* 4.0 26.2 - - + -
207A ALA* 4.7 2.0 - - + -
351A ILE* 2.9 35.8 + - + +
352A LEU* 3.8 6.1 - - - +
354A PHE* 1.3 82.3 - - + +
356A LEU* 1.3 63.2 + - + +
358A SER* 2.7 23.1 + - - +
360A ASP* 3.5 31.3 + - + +
367A LEU* 3.9 26.2 - - + -
370A ASP* 5.3 1.8 - - + -
371A LEU* 4.8 5.6 - - + -
374A MET* 5.0 3.6 - - + -
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Residues in contact with LEU 356 (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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325A ILE* 3.9 6.1 - - + +
328A CYS* 3.6 33.0 - - + -
329A LYS* 3.7 37.7 - - + +
332A VAL* 4.1 17.6 - - + +
352A LEU* 3.0 30.3 + - + +
353A HIS 3.9 3.1 - - - +
354A PHE 3.3 0.2 - - - -
355A LEU* 1.3 77.0 - - + +
357A ALA* 1.3 61.4 + - - +
358A SER 3.4 0.5 + - - -
359A GLY* 3.4 11.4 + - - -
360A ASP* 4.6 6.1 + - + +
367A LEU* 3.9 22.2 - - + -
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Residues in contact with ALA 357 (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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332A VAL* 4.1 15.8 - - + +
335A GLU* 4.2 5.4 - - - +
339A PHE* 3.6 17.8 - - + +
343A TYR* 3.3 47.6 - - + +
353A HIS 3.0 10.7 + - - +
356A LEU* 1.3 78.4 - - - +
358A SER* 1.3 60.2 + - - +
359A GLY 3.2 1.0 + - - -
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Residues in contact with SER 358 (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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203A ALA 5.5 1.6 + - - -
339A PHE* 3.4 34.7 - - - -
354A PHE* 3.0 21.4 + - - -
355A LEU* 2.7 23.1 + - - +
356A LEU 3.2 0.4 - - - -
357A ALA* 1.3 76.4 - - - +
359A GLY* 1.3 60.2 + - - +
360A ASP* 3.7 11.3 + - - +
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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