Contacts of the strand formed by residues 190 - 194 (chain A) in PDB entry 1H3F
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 VAL 190 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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28A LEU* 4.2 18.4 - - + -
31A LYS* 5.4 0.4 - - + -
38A LEU* 4.5 8.7 - - + -
39A THR 3.1 3.5 + - - +
40A VAL* 4.3 20.0 - - + -
41A LYS* 2.8 27.9 + - - +
65A PHE* 4.3 18.8 - - + -
188A ALA* 4.0 3.6 - - - +
189A ASP* 1.3 92.6 - - + +
191A GLU* 1.3 66.1 + - - +
192A MET* 4.4 0.7 - - - -
216A GLN* 4.6 0.9 - - - -
217A VAL* 3.3 24.5 - - + +
219A PHE* 3.9 25.4 - - + -
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Residues in contact with GLU 191 (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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41A LYS* 3.2 44.7 + - + +
43A GLY 5.1 0.3 + - - -
179A GLN* 3.0 24.9 + - - +
180A ALA* 5.9 0.3 - - - -
183A SER* 3.5 0.2 + - - -
190A VAL* 1.3 77.4 - - - +
192A MET* 1.3 73.9 + - - +
200A ASN 4.9 0.5 - - - +
201A LEU* 3.5 27.2 - - + +
204A GLY* 5.2 0.9 - - - -
216A GLN* 2.7 44.1 + - - +
217A VAL 3.0 8.9 + - - +
218A CYS* 5.4 0.2 - - - -
219A PHE 3.0 24.1 + - - -
1433A TYE 3.6 5.9 - - - -
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Residues in contact with MET 192 (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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40A VAL* 3.6 23.8 - - + -
41A LYS 2.8 14.9 + - - +
42A LEU* 4.0 16.0 - - + +
43A GLY 5.4 0.3 + - - -
58A VAL* 3.9 21.1 - - + +
61A LYS* 3.7 31.6 - - + -
62A MET* 3.6 22.2 - - + -
65A PHE* 4.0 10.8 - - - -
190A VAL* 4.4 1.1 - - - -
191A GLU* 1.3 86.6 - - - +
193A GLY* 1.3 57.7 + - - +
197A GLN* 5.8 0.7 + - - -
201A LEU* 4.1 5.4 - - - +
219A PHE* 3.5 35.4 - - + +
221A MET* 4.1 11.4 - - + -
1433A TYE 6.0 0.9 - - - -
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Residues in contact with GLY 193 (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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42A LEU* 5.2 3.1 - - - -
58A VAL* 4.0 14.5 - - - +
192A MET* 1.3 77.1 - - - +
194A GLY* 1.3 64.0 + - - -
197A GLN* 4.4 8.5 - - - -
201A LEU* 4.3 9.2 - - - -
219A PHE 3.0 7.6 + - - +
220A LEU* 3.2 7.1 - - - -
221A MET 2.9 23.4 + - - -
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Residues in contact with GLY 194 (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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58A VAL* 4.3 7.7 - - - +
193A GLY* 1.3 76.7 - - - +
195A THR* 1.3 59.2 + - - -
196A ASP* 3.0 17.4 + - - -
197A GLN* 2.9 27.2 + - - +
220A LEU* 3.6 6.9 - - - +
221A MET* 3.4 10.1 - - - -
223A LEU* 4.0 11.2 - - - -
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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