Contacts of the helix formed by residues 197 - 202 (chain A) in PDB entry 5GJD
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 197 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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195A TRP 3.7 1.4 + - - -
196A MET* 1.3 75.5 - - - +
198A PRO* 1.3 74.2 - - + +
199A GLU* 3.5 27.4 - - - +
200A VAL* 3.1 15.5 + - + +
201A PHE* 3.4 10.6 + - - -
210A CYS* 3.8 22.4 + - + +
213A PHE* 3.5 24.7 - - + -
274A ARG* 4.0 0.2 - - - +
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Residues in contact with PRO 198 (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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196A MET 3.7 0.9 - - - +
197A ALA* 1.3 85.2 - - + +
199A GLU* 1.3 67.1 + - - +
200A VAL 3.3 0.2 + - - -
201A PHE* 3.4 24.9 + - + -
202A GLU* 3.0 35.8 + - - +
213A PHE* 3.6 25.6 - - + -
243A VAL* 4.2 7.6 - - + +
244A HIS* 4.6 11.0 - - + -
248A ARG* 4.3 16.4 - - - +
269A LYS* 4.7 11.0 - - + +
274A ARG* 4.0 5.2 - - - +
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Residues in contact with GLU 199 (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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197A ALA* 3.5 15.6 - - - +
198A PRO* 1.3 76.5 - - - +
200A VAL* 1.3 58.6 + - - +
202A GLU* 3.7 15.1 + - - +
204A SER* 3.1 43.6 + - - +
205A ASN 4.5 3.4 - - - +
206A TYR* 4.2 21.2 - - + +
207A SER* 5.1 1.8 + - - +
209A LYS* 5.0 0.2 - - - +
210A CYS* 3.8 12.0 + - - +
269A LYS 4.2 1.7 - - - +
271A PRO* 3.8 22.5 - - + +
274A ARG* 2.8 45.0 + - - -
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Residues in contact with VAL 200 (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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155A ARG* 3.5 40.3 + - + +
196A MET* 3.9 17.9 - - + -
197A ALA* 3.1 15.0 + - + +
199A GLU* 1.3 77.3 - - + +
201A PHE* 1.3 60.5 + - - +
203A GLY* 3.0 21.7 + - - -
204A SER 4.4 0.9 + - - +
206A TYR* 3.6 27.3 - - + -
210A CYS* 3.5 34.8 - - + -
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Residues in contact with PHE 201 (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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193A ALA 4.7 4.0 - - - -
196A MET* 3.5 44.6 - - + -
197A ALA 3.4 10.9 + - - -
198A PRO* 3.4 28.3 - - + -
200A VAL* 1.3 79.9 - - - +
202A GLU* 1.3 62.2 + - - +
203A GLY 3.2 1.8 + - - -
240A MET* 3.3 72.8 - - + +
243A VAL* 4.0 13.2 - - + -
244A HIS* 4.1 15.3 - + + -
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Residues in contact with GLU 202 (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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198A PRO* 3.0 22.5 + - - +
199A GLU* 3.7 12.0 + - - +
200A VAL 3.2 0.4 - - - -
201A PHE* 1.3 78.4 - - + +
203A GLY* 1.3 59.7 + - - +
204A SER* 2.8 26.1 + - - +
244A HIS* 3.1 37.8 + - + +
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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