Contacts of the helix formed by residues 281 - 285 (chain A) in PDB entry 1N35
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 THR 281 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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277A PHE 2.6 22.2 + - - +
278A PRO* 3.3 1.8 + - - +
279A GLN 3.3 2.2 - - - -
280A ASN* 1.3 86.9 - - - +
282A LEU* 1.3 77.4 + - - +
283A HIS 3.3 0.2 - - - -
284A SER 2.8 11.3 + - - -
285A MET* 2.8 22.8 + - - +
347A LEU* 4.5 9.9 - - + -
351A THR* 3.6 14.8 - - - +
364A TYR* 3.7 23.3 - - + +
365A ILE* 4.3 11.5 - - - +
368A ALA* 3.8 26.2 - - + +
369A MET* 4.6 1.2 - - - +
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Residues in contact with LEU 282 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278A PRO* 3.1 10.0 + - + +
281A THR* 1.3 84.1 + - - +
283A HIS* 1.3 83.7 + - + +
284A SER 3.1 2.9 + - - -
285A MET* 3.5 18.1 + - - +
365A ILE* 3.9 24.3 - - + +
369A MET* 3.8 22.2 - - + -
776A ASP 4.9 1.6 - - - +
778A THR* 3.5 28.7 + - + +
785A TYR* 4.0 25.4 - - + -
786A PHE 4.7 2.7 - - - +
787A ILE* 3.9 22.0 - - + +
792A ILE* 4.3 11.2 - - + -
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Residues in contact with HIS 283 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278A PRO* 3.1 27.8 + - + +
279A GLN* 3.0 37.2 - - + +
282A LEU* 1.3 100.5 - - + +
284A SER* 1.3 62.1 + - - +
285A MET 3.7 0.7 - - - -
322A ARG* 3.0 28.7 + - - -
327A ASN* 3.6 5.7 - - - +
583A ASN* 5.8 0.2 - - - -
776A ASP* 3.2 38.8 + - + -
778A THR* 3.9 12.5 + - + -
780A GLU* 4.0 17.3 + - - -
785A TYR* 6.0 0.4 - - - -
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Residues in contact with SER 284 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279A GLN 2.6 24.8 + - - -
280A ASN* 4.0 5.1 - - - -
281A THR 2.8 12.6 + - - -
283A HIS* 1.3 69.5 - - - +
285A MET* 1.3 65.5 + - - +
286A TYR 3.7 0.9 + - - -
287A GLU* 4.0 16.7 + - - +
322A ARG* 3.9 10.1 - - - +
327A ASN* 3.0 7.6 + - - -
348A ARG* 3.0 30.7 + - - -
351A THR* 3.3 21.3 - - - +
352A LYS* 6.2 0.6 - - - +
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Residues in contact with MET 285 (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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281A THR* 2.8 28.7 - - - +
282A LEU 3.5 5.4 + - - +
283A HIS 3.7 0.6 - - - -
284A SER* 1.3 78.1 - - - +
286A TYR* 1.3 108.8 + - + +
322A ARG* 3.4 18.1 - - - +
351A THR* 3.6 17.5 - - - -
354A TYR* 4.0 23.1 - - + -
361A SER* 4.1 13.7 - - - +
364A TYR* 4.4 7.0 - - + -
365A ILE* 3.4 35.9 - - + -
787A ILE* 3.7 11.0 - - + +
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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