Contacts of the helix formed by residues 193 - 198 (chain s) in PDB entry 3J7Y
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 193 (chain s).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1935 LEU* 6.6 0.4 - - + -
189s SER 3.8 6.3 - - - +
190s PRO 5.2 2.2 - - - +
191s HIS 4.7 0.7 - - - -
192s ASN* 1.3 84.9 - - + +
194s ALA* 1.3 65.3 + - + +
195s LEU 3.4 0.4 - - - -
196s ALA* 3.5 19.1 + - + +
197s ALA* 3.6 7.3 + - - +
428s ARG* 3.3 20.6 - - - +
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Residues in contact with ALA 194 (chain s).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192s ASN* 3.3 13.3 - - - +
193s PRO* 1.3 82.5 - - + +
195s LEU* 1.3 55.9 + - + +
197s ALA* 3.2 7.3 + - - +
198s ALA* 2.7 36.6 + - - +
243s ILE* 4.7 12.2 - - + +
427s ASN 5.9 0.2 - - - +
428s ARG* 5.7 0.7 - - + -
429s PRO* 4.0 30.7 - - + -
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Residues in contact with LEU 195 (chain s).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1865 GLN* 5.3 2.8 + - - +
185s VAL* 4.3 49.5 - - + +
188s LEU* 4.7 12.8 - - + +
189s SER* 5.2 1.3 - - - -
192s ASN* 3.8 28.9 + - + +
193s PRO 3.4 0.6 - - - -
194s ALA* 1.3 77.0 - - + +
196s ALA* 1.3 64.9 + - - +
198s ALA* 3.4 21.1 - - + +
241s ILE* 4.8 6.6 - - + +
243s ILE* 6.0 0.9 - - + -
296s HIS* 3.8 21.1 - - + +
425s LEU* 3.6 43.7 - - + +
427s ASN 5.1 1.3 - - - +
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Residues in contact with ALA 196 (chain s).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1865 GLN* 5.8 3.5 - - - +
1875 LEU* 5.6 4.5 - - - +
1905 SER* 3.7 35.8 - - - +
1935 LEU* 6.3 0.7 - - + -
185s VAL* 6.0 0.4 - - - -
189s SER* 3.6 24.9 + - - +
192s ASN 4.3 2.0 + - - -
193s PRO* 3.5 15.6 + - + +
194s ALA 3.3 0.4 - - - -
195s LEU* 1.3 79.5 - - - +
197s ALA* 1.3 61.1 + - - +
198s ALA 4.2 2.3 - - - +
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Residues in contact with ALA 197 (chain s).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193s PRO 3.6 7.7 + - - +
194s ALA* 3.2 10.4 + - - +
196s ALA* 1.3 80.2 - - - +
198s ALA* 1.3 64.4 + - - +
199s ALA* 3.5 1.7 + - - -
243s ILE* 6.3 1.1 - - + -
244s SER* 5.8 3.8 - - - +
292s CYS* 4.6 7.7 - - - -
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Residues in contact with ALA 198 (chain s).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1865 GLN* 4.6 10.2 + - - +
194s ALA 2.7 21.6 + - - +
195s LEU* 3.4 21.0 + - + +
196s ALA 3.4 3.0 - - - +
197s ALA* 1.3 75.1 - - - +
199s ALA* 1.3 61.9 + - - +
200s LEU* 4.0 0.5 + - - +
241s ILE* 4.1 13.1 - - + +
242s ARG 3.5 13.0 - - - +
243s ILE* 4.0 26.5 - - + +
244s SER 5.5 0.4 - - - +
292s CYS* 4.8 1.8 - - - -
296s HIS* 5.4 0.2 - - + -
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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