Contacts of the helix formed by residues 332 - 339 (chain A) in PDB entry 1O86
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 PRO 332 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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330A PRO 3.9 1.6 - - - +
331A VAL* 1.3 88.7 - - + +
333A PRO* 1.3 77.9 - - + +
334A GLU* 4.2 7.0 - - + +
335A PHE* 2.8 26.9 + - + +
336A TRP* 3.9 3.1 - - - -
363A LYS* 4.0 24.2 - - + +
365A PHE* 4.0 20.9 - - + -
388A ILE* 5.4 0.7 - - + -
392A MET* 3.6 18.2 - - - -
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Residues in contact with PRO 333 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331A VAL 4.4 1.8 - - - +
332A PRO* 1.3 85.3 - - + +
334A GLU* 1.3 61.8 + - - +
335A PHE 3.1 1.2 + - - -
336A TRP* 3.1 25.9 + - + +
337A ASN* 3.5 8.7 + - - +
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Residues in contact with GLU 334 (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 PRO* 4.7 4.3 - - + -
333A PRO* 1.3 80.9 - - - +
335A PHE* 1.3 61.1 + - - +
337A ASN* 3.2 8.1 + - + +
338A LYS* 2.6 66.9 + - + +
361A ASN* 5.5 0.5 + - - -
363A LYS* 3.3 35.8 - - - +
364A ASP* 3.7 18.9 + - - +
365A PHE 5.1 0.4 - - - +
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Residues in contact with PHE 335 (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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316A PHE* 4.6 5.6 - + + -
331A VAL* 3.6 33.2 - - + -
332A PRO* 2.8 23.3 + - + +
334A GLU* 1.3 79.0 - - - +
336A TRP* 1.3 86.2 + + - -
338A LYS* 5.4 0.4 - - - -
339A SER* 2.8 57.0 + - - +
341A LEU* 4.6 4.3 - - + -
365A PHE* 3.4 30.9 + - + +
366A ARG* 4.1 1.3 - - - -
367A ILE* 3.7 32.3 - - + -
385A MET* 3.8 20.9 - - - -
388A ILE* 4.2 11.2 - - + -
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Residues in contact with TRP 336 (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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313A ARG* 3.1 55.1 + - + +
316A PHE* 3.8 24.7 - - + -
317A LYS* 3.5 64.4 - - + +
320A ASP* 4.3 13.7 + - + -
331A VAL* 3.5 30.8 + - + +
332A PRO 3.9 8.4 + - - -
333A PRO* 3.1 18.9 + - + +
335A PHE* 1.3 90.5 - + - +
337A ASN* 1.3 60.8 + - - +
339A SER* 4.4 7.8 + - - +
341A LEU* 4.2 11.4 - - + +
385A MET* 5.2 0.4 - - + -
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Residues in contact with ASN 337 (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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333A PRO 3.5 7.2 + - - +
334A GLU* 3.2 11.8 + - + +
335A PHE 3.2 0.6 - - - -
336A TRP* 1.3 81.7 - - - +
338A LYS* 1.3 72.9 + - + +
339A SER 4.6 1.8 - - - +
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Residues in contact with LYS 338 (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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67A TRP* 3.3 18.9 + - - -
334A GLU* 2.6 49.4 + - + +
337A ASN* 1.3 89.2 - - - +
339A SER* 1.3 67.6 + - - +
364A ASP* 3.3 12.1 + - - +
366A ARG* 3.5 43.2 + - + +
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Residues in contact with SER 339 (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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67A TRP* 4.3 0.2 - - - -
335A PHE* 2.8 37.0 + - - -
336A TRP 4.4 6.1 + - - +
337A ASN 3.7 3.5 - - - +
338A LYS* 1.3 80.7 - - - +
340A MET* 1.3 59.6 + - - +
341A LEU* 3.7 23.0 + - - +
366A ARG* 3.4 9.6 - - - +
367A ILE 3.0 30.1 + - - -
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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