Contacts of the strand formed by residues 194 - 199 (chain A) in PDB entry 1HRE
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 GLY 194 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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190A CYS* 4.8 2.0 - - - -
192A ASN 3.3 3.2 + - - -
193A GLY* 1.3 88.0 - - - +
195A GLU* 1.3 79.7 + - - +
196A CYS 3.8 2.2 + - - -
210A CYS* 4.5 6.3 - - - -
211A LYS 3.2 14.1 - - - -
213A GLN* 3.1 8.9 + - - +
216A PHE* 4.6 5.1 - - - -
221A CYS* 3.8 23.8 - - - -
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Residues in contact with GLU 195 (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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181A LYS* 5.1 13.7 - - + +
194A GLY* 1.3 90.8 - - - +
196A CYS* 1.3 59.7 + - - +
197A PHE* 2.7 45.5 - - + -
209A LEU 3.0 5.9 - - - +
210A CYS* 3.6 3.5 - - - +
211A LYS* 3.1 30.2 + - + +
213A GLN* 2.4 45.4 + - + +
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Residues in contact with CYS 196 (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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181A LYS* 3.3 7.1 - - - +
182A CYS* 2.0 66.0 + - + -
186A GLU 3.5 15.9 - - - -
187A LYS* 4.2 9.0 - - + -
189A PHE* 4.2 5.2 - - - -
190A CYS* 3.9 4.7 - - - -
194A GLY 3.8 1.4 - - - -
195A GLU* 1.3 77.2 - - - +
197A PHE* 1.3 64.6 + - - +
208A TYR* 3.6 13.9 - - - -
209A LEU 3.2 7.0 - - - -
210A CYS* 3.4 22.3 - - - -
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Residues in contact with PHE 197 (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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179A LEU* 3.3 36.8 - - + -
181A LYS* 3.2 37.9 - - + +
182A CYS* 3.4 3.7 - - - -
195A GLU* 2.7 42.6 - - + -
196A CYS* 1.3 73.0 - - - +
198A MET* 1.3 58.6 + - - +
207A ARG* 2.4 36.0 - - + +
208A TYR* 3.2 5.9 - - - -
209A LEU* 2.8 20.3 + - + +
211A LYS* 5.2 5.6 - - + -
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Residues in contact with MET 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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179A LEU* 2.7 24.7 - - - +
180A VAL* 3.0 26.7 - - + +
181A LYS 4.6 1.5 - - - +
182A CYS* 4.1 21.3 - - - +
186A GLU* 4.0 19.7 - - - +
197A PHE* 1.3 77.2 - - - +
199A VAL* 1.3 61.1 + - - +
206A SER* 4.7 9.2 - - - +
207A ARG 4.3 6.5 - - - +
208A TYR* 3.1 37.9 - - + +
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Residues in contact with VAL 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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178A HIS* 6.0 3.8 - - + +
179A LEU* 3.3 37.9 - - + +
180A VAL* 5.3 1.3 - - - -
198A MET* 1.3 79.0 - - - +
200A LYS* 1.3 85.1 + - + +
201A ASP 4.0 8.5 - - - +
202A LEU* 4.1 21.1 - - + -
205A PRO* 3.3 29.2 - - + +
206A SER* 3.8 8.7 + - - +
207A ARG* 4.2 22.1 - - + +
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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