Contacts of the helix formed by residues 350 - 354 (chain A) in PDB entry 2J2M
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 350 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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348A GLY* 3.2 0.8 - - - -
349A PRO* 1.3 76.2 - - - +
351A TYR* 1.3 63.7 + - - +
352A GLN* 3.1 4.0 - - - -
353A GLN* 2.8 48.7 + - - +
369A ASP 3.0 20.4 + - - +
370A GLY 3.0 7.4 + - - -
371A ALA 2.9 26.5 + - - +
372A MET 4.1 3.8 - - - +
373A PRO* 3.7 11.3 - - - +
44C HIS* 2.7 30.8 + - - -
372C MET* 3.4 14.6 - - + +
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Residues in contact with TYR 351 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314A GLY* 5.0 5.2 - - - -
340A SER* 3.2 30.1 + - - -
343A GLN* 3.3 34.0 + - + -
344A ARG* 4.0 27.1 + - + -
347A ILE* 3.6 33.4 - - + -
348A GLY 3.0 24.6 + - - +
349A PRO 3.3 5.5 - - - -
350A ASN* 1.3 76.8 - - - +
352A GLN* 1.3 90.1 + - + +
353A GLN 3.2 1.2 + - - -
354A LEU* 3.2 11.5 + - - +
357A ASN* 3.2 29.8 + - - -
12C GLN* 4.4 10.0 + - - -
36C TYR* 4.6 2.1 + - - -
372C MET* 4.2 9.9 - - - -
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Residues in contact with GLN 352 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116A LYS* 4.9 5.0 + - - -
123A ASN* 4.4 0.4 - - - +
314A GLY 4.9 0.9 - - - +
349A PRO 5.2 0.4 + - - +
350A ASN* 3.0 2.9 + - - -
351A TYR* 1.3 104.8 - - + +
353A GLN* 1.3 61.0 + - + +
354A LEU 3.4 0.4 - - - -
357A ASN* 3.0 42.3 + - - +
358A CYS* 3.7 16.3 - - - +
359A PRO* 4.1 6.8 - - - +
11C ASN* 3.1 46.7 + - + +
12C GLN* 3.5 35.1 + - - +
36C TYR* 5.2 0.2 - - - +
40C GLU* 5.1 0.7 - - - +
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Residues in contact with GLN 353 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350A ASN* 2.8 46.2 + - + +
352A GLN* 1.3 79.0 - - + +
354A LEU* 1.3 61.7 + - - +
355A PRO* 3.6 0.7 - - - +
358A CYS* 4.6 10.0 - - - +
369A ASP 5.0 2.0 + - - -
372A MET 4.1 0.9 - - - +
373A PRO* 3.7 2.9 - - - +
374A PHE* 3.3 13.5 + - - +
375A LYS* 3.0 57.1 + - + +
376A GLN* 4.3 5.9 + - - +
44C HIS* 5.3 0.6 + - - -
372C MET* 5.1 2.2 - - + +
374C PHE* 2.9 26.6 - - + -
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Residues in contact with LEU 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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308A ALA 6.0 0.2 - - - +
312A SER* 4.2 16.8 - - - -
347A ILE* 3.4 33.0 - - + -
351A TYR 3.2 12.0 + - - +
353A GLN* 1.3 78.1 - - - +
355A PRO* 1.3 75.3 - - + +
356A ILE* 4.5 5.2 - - + +
357A ASN* 2.8 23.1 + - - +
358A CYS* 3.0 9.6 + - - -
372C MET* 3.8 47.6 - - + -
373C PRO* 4.0 12.1 - - + +
374C PHE* 4.0 19.1 - - + -
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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