Contacts of the helix formed by residues 344 - 354 (chain A) in PDB entry 1NRX
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 344 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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342A HIS 3.7 4.8 + - - -
343A CYS* 1.3 77.7 - - - +
345A VAL* 1.3 59.7 + - - +
346A ASP* 3.0 11.8 + - - +
347A GLN* 2.6 41.4 + - - +
348A LEU* 3.0 26.9 + - - +
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Residues in contact with VAL 345 (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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344A SER* 1.3 75.3 - - - +
346A ASP* 1.3 64.2 + - - +
348A LEU* 4.1 1.6 - - - +
349A MET* 2.9 34.0 + - + +
388A ARG* 3.3 52.7 - - + +
391A LEU* 4.0 15.6 - - + +
392A ALA* 3.3 33.9 - - - +
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Residues in contact with ASP 346 (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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344A SER* 3.0 6.7 + - - +
345A VAL* 1.3 81.1 + - - +
347A GLN* 1.3 55.1 + - - +
348A LEU 3.1 0.2 - - - -
349A MET* 2.9 3.5 + - - +
350A PHE* 2.5 39.3 + - - +
388A ARG* 3.2 31.1 + - - +
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Residues in contact with GLN 347 (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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280A ILE* 3.3 24.2 - - + +
342A HIS 5.4 1.3 - - - +
343A CYS* 5.1 0.2 - - - -
344A SER* 2.6 33.1 + - - +
346A ASP* 1.3 73.1 - - - +
348A LEU* 1.3 52.3 + - - +
350A PHE* 3.5 18.5 + - - +
351A ASN* 2.6 53.6 + - - +
609A CL 3.2 17.3 - - - +
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Residues in contact with LEU 348 (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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273A ILE* 5.3 2.9 - - + -
276A ALA* 3.4 25.6 - - + +
277A ILE* 4.2 11.7 - - + +
280A ILE* 3.4 16.8 - - + -
329A LEU* 4.5 15.0 - - + -
343A CYS* 3.1 35.0 - - + +
344A SER 3.0 25.5 + - - +
345A VAL 4.2 0.2 - - - +
347A GLN* 1.3 74.4 - - - +
349A MET* 1.3 61.8 + - - +
351A ASN* 3.2 3.1 + - - +
352A MET* 3.0 34.0 + - - +
391A LEU* 3.5 36.6 - - + -
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Residues in contact with MET 349 (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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345A VAL* 2.9 27.4 + - + +
346A ASP* 2.9 8.0 + - - +
348A LEU* 1.3 77.3 - - - +
350A PHE* 1.3 62.3 + - - +
352A MET* 3.4 11.2 + - - +
353A ALA* 3.3 17.8 + - - +
363A LYS* 3.7 22.1 + - - +
384A ASN* 3.2 52.7 - - + +
387A ILE* 3.7 25.8 - - + -
388A ARG* 4.0 28.3 - - + +
391A LEU* 4.4 4.5 - - + -
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Residues in contact with PHE 350 (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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346A ASP 2.5 19.8 + - - +
347A GLN* 3.6 21.3 - - - +
349A MET* 1.3 75.7 - - - +
351A ASN* 1.3 70.5 + - - +
353A ALA* 3.2 23.9 - - + +
354A LEU* 3.2 29.1 - - + +
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Residues in contact with ASN 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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275A HIS* 5.7 0.7 - - - +
276A ALA* 3.5 34.8 + - - -
279A ALA* 4.1 8.2 - - + +
280A ILE* 3.6 11.7 - - - +
347A GLN* 2.6 41.8 + - - +
348A LEU* 3.2 4.9 + - - +
350A PHE* 1.3 81.6 - - - +
352A MET* 1.3 63.1 + - - +
353A ALA 3.1 2.6 + - - -
354A LEU* 3.5 20.6 + - + +
355A ASP* 3.5 14.2 - - - -
609A CL 3.2 18.6 - - - +
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Residues in contact with MET 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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272A SER* 3.7 37.0 - - - +
273A ILE* 4.0 21.8 - - + -
276A ALA* 3.5 17.5 - - + +
348A LEU 3.0 20.3 + - - +
349A MET* 3.7 6.7 - - - +
350A PHE 3.3 0.4 - - - -
351A ASN* 1.3 76.0 - - - +
353A ALA* 1.3 63.9 + - - +
355A ASP* 3.6 18.8 + - - +
361A PRO 5.6 0.5 - - - -
363A LYS* 3.2 35.2 - - + +
365A ILE* 4.3 2.7 - - + -
387A ILE* 4.0 36.6 - - + -
391A LEU* 4.8 4.9 - - - -
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Residues in contact with ALA 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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349A MET 3.3 11.2 + - - +
350A PHE* 3.2 20.6 + - + +
351A ASN 3.1 0.2 - - - -
352A MET* 1.3 75.0 - - - +
354A LEU* 1.3 61.0 + - + +
355A ASP* 2.8 17.1 + - - -
361A PRO* 4.3 25.0 - - + +
363A LYS* 4.2 9.8 - - - +
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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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350A PHE* 3.2 40.4 - - + +
351A ASN* 3.5 21.9 + - + +
352A MET 3.3 1.0 - - - -
353A ALA* 1.3 78.4 - - + +
355A ASP* 1.3 61.2 + - - +
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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