Contacts of the helix formed by residues 241 - 245 (chain A) in PDB entry 1ZSV
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 ALA 241 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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218A VAL 3.3 15.0 - - - +
219A GLY* 4.4 5.6 - - - -
238A ILE* 6.3 0.4 - - + -
240A GLY* 1.3 74.7 - - - +
242A ILE* 1.3 65.5 + - - +
243A SER 3.2 3.1 - - - -
244A THR* 2.8 29.1 + - + +
245A TYR* 3.1 18.9 + - + -
257B PRO* 3.5 34.3 - - + -
261B ILE* 4.2 0.9 - - + +
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Residues in contact with ILE 242 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A PRO* 3.7 33.9 - - + -
149A ALA* 3.9 25.8 - - + -
217A ASN* 3.0 22.7 + - + +
218A VAL* 3.4 14.5 + - + -
240A GLY* 5.6 0.7 - - - -
241A ALA* 1.3 74.9 - - - +
243A SER* 1.3 59.7 + - - +
244A THR 2.9 6.1 + - - -
245A TYR* 3.1 32.4 + - + +
246A ASN* 4.6 7.1 + - - +
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Residues in contact with SER 243 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218A VAL* 2.5 33.6 + - - -
219A GLY 3.6 12.1 + - - -
220A GLY* 3.9 3.6 + - - -
222A PHE* 6.3 0.2 - - - -
242A ILE* 1.3 79.5 - - - +
244A THR* 1.3 63.8 + - - +
245A TYR 3.6 0.2 - - - -
246A ASN* 5.0 1.8 + - - +
247A ARG* 5.0 5.7 + - - +
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Residues in contact with THR 244 (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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220A GLY* 4.4 15.0 - - - +
241A ALA* 2.8 33.7 + - + +
243A SER* 1.3 88.7 - - - +
245A TYR* 1.3 64.0 + - - +
246A ASN 3.2 4.1 + - - -
247A ARG* 2.9 44.3 + - - +
251A LEU* 3.9 20.0 - - + -
252A PRO* 4.8 6.7 - - + -
257B PRO* 3.9 7.9 - - + +
258B GLU* 3.7 13.0 + - - -
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Residues in contact with TYR 245 (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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48A PRO* 3.8 29.6 - - + -
49A TYR* 4.7 3.6 - - - -
51A ARG* 3.3 38.8 + - + +
52A VAL* 3.4 30.9 - - + +
55A LYS* 5.7 2.3 - - - +
239A CYS 4.8 0.3 + - - -
240A GLY* 3.4 11.3 - - - -
241A ALA* 3.1 40.8 + - + -
242A ILE* 3.1 34.6 + - + +
244A THR* 1.3 81.5 - - - +
246A ASN* 1.3 62.3 + - - +
247A ARG* 3.5 2.0 + - - +
317A LEU* 5.7 2.0 - - + -
258B GLU* 3.8 19.9 - - + -
261B ILE* 4.6 5.3 - - + +
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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