Contacts of the strand formed by residues 191 - 196 (chain Z) in PDB entry 5V04
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 ASN 191 (chain Z).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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17Z ILE 3.9 4.9 - - - +
18Z HIS* 3.5 17.4 + - - -
185Z LYS 3.2 4.5 - - - +
186Z MET* 3.2 19.3 - - - -
187Z ASP* 2.8 33.0 + - - +
189Z PHE* 4.2 13.6 - - - +
190Z GLY* 1.3 74.1 - - - +
192Z GLY* 1.3 59.2 + - - +
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Residues in contact with GLY 192 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16Z PRO* 3.5 5.5 - - - +
17Z ILE* 2.8 39.4 + - - +
19Z VAL* 6.3 0.2 - - - -
183Z ILE* 4.4 8.1 - - - -
184Z LEU 3.9 1.6 - - - -
185Z LYS 3.5 8.7 - - - -
186Z MET* 4.2 8.5 - - - -
190Z GLY 3.3 3.5 + - - -
191Z ASN* 1.3 75.5 - - - +
193Z LEU* 1.3 60.5 + - - +
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Residues in contact with LEU 193 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7Z LEU* 4.4 21.1 - - + -
14Z SER* 3.8 21.1 - - - +
15Z GLU* 3.6 30.3 - - - +
16Z PRO* 3.8 11.9 - - + -
182Z VAL 3.7 0.5 - - - +
183Z ILE* 4.4 2.7 - - - +
184Z LEU* 2.7 51.9 + - + +
185Z LYS* 4.6 22.9 - - + -
192Z GLY* 1.3 73.8 - - - -
194Z GLU* 1.3 58.2 + - - +
195Z ILE* 4.0 2.2 + - + +
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Residues in contact with GLU 194 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14Z SER* 3.4 1.7 - - - -
15Z GLU 2.9 33.6 + - - +
17Z ILE* 3.2 39.2 - - + +
21Z LYS* 3.7 16.4 + - - +
22Z TYR* 2.5 32.7 + - - -
181Z LYS* 4.1 3.9 + - - +
182Z VAL 3.3 11.2 - - - +
183Z ILE* 4.2 5.8 - - + +
192Z GLY 4.1 0.8 - - - -
193Z LEU* 1.3 72.7 - - - +
195Z ILE* 1.3 65.2 + - - +
196Z ASP* 2.8 32.3 - - - +
199Z ARG* 3.2 12.8 + - - +
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Residues in contact with ILE 195 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7Z LEU* 3.6 31.9 - - + -
10Z ILE* 4.6 15.7 - - + +
13Z ALA* 3.9 16.8 - - + +
14Z SER* 3.7 19.7 - - - -
175Z LEU* 4.1 36.1 - - + +
180Z LYS 3.8 0.7 - - - +
181Z LYS* 3.8 1.0 - - - -
182Z VAL* 2.8 37.7 + - + +
184Z LEU* 3.9 16.2 - - + -
193Z LEU* 4.8 2.9 - - + +
194Z GLU* 1.3 77.5 - - - +
196Z ASP* 1.3 72.5 + - - +
197Z GLN 4.2 0.2 + - - -
200Z LEU* 4.8 2.0 - - + -
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Residues in contact with ASP 196 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13Z ALA 4.0 2.3 + - - +
175Z LEU* 5.6 0.7 - - - -
180Z LYS 3.3 3.8 - - - +
181Z LYS* 3.3 31.2 - - - +
194Z GLU* 2.8 34.4 - - - +
195Z ILE* 1.3 81.0 - - - +
197Z GLN* 1.3 66.5 + - - +
198Z ALA* 4.3 8.5 - - + +
199Z ARG* 3.3 41.6 + - + +
200Z LEU* 3.6 11.1 + - - +
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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