Contacts of the strand formed by residues 194 - 198 (chain A) in PDB entry 1UHG
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 GLN 194 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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191A GLU 5.4 2.4 + - - +
192A ASP 3.7 12.8 - - - +
193A THR* 1.3 78.7 - - - +
195A ALA* 1.3 67.9 + - - +
196A MET* 3.4 14.8 + - + +
209A GLN* 4.0 6.5 - - - +
210A MET* 2.8 36.8 + - - +
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Residues in contact with ALA 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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194A GLN* 1.3 77.5 - - - +
196A MET* 1.3 63.7 + - - +
207A PRO* 4.8 13.7 - - + -
208A VAL 3.4 8.5 - - - +
209A GLN* 3.6 14.7 + - - +
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Residues in contact with MET 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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194A GLN* 3.7 22.7 - - + +
195A ALA* 1.3 81.0 - - - +
197A PRO* 1.3 76.2 - - + +
207A PRO* 4.1 3.8 - - - +
208A VAL* 2.8 32.9 + - - +
210A MET* 3.5 44.6 - - + +
212A TYR* 6.2 0.2 - - - -
281A TYR* 3.9 17.5 - - + -
359A ARG* 3.5 33.7 - - + +
361A ASP* 5.0 5.8 - - + +
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Residues in contact with PRO 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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196A MET* 1.3 92.7 - - + +
198A PHE* 1.3 60.3 + - - +
199A ARG* 3.9 16.7 + - + +
205A SER* 3.5 20.6 - - - +
206A LYS 3.6 7.4 - - - +
207A PRO* 4.1 3.4 - - + -
208A VAL* 4.8 0.4 - - - -
210A MET* 4.8 0.9 - - - +
361A ASP* 3.7 18.9 - - - +
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Residues in contact with PHE 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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197A PRO* 1.3 73.9 - - - +
199A ARG* 1.3 65.2 + - - +
200A VAL* 3.1 10.7 + - + +
205A SER* 2.8 17.3 - - - -
206A LYS* 2.8 24.1 + - + +
208A VAL* 3.7 24.0 - - + -
210A MET* 4.4 1.3 - - + -
283A PRO* 4.2 1.8 - - + -
360A ALA 3.2 21.3 - - - -
361A ASP* 3.4 14.4 - - - -
362A HIS* 3.3 33.7 - - - -
363A PRO* 3.7 7.4 - - + -
364A PHE* 3.9 16.6 - + - -
382A CYS 4.3 2.7 - - - -
383A VAL 3.6 26.9 - - - -
385A PRO* 3.9 32.1 - - + -
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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