Contacts of the strand formed by residues 193 - 199 (chain A) in PDB entry 1VJZ
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 THR 193 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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161A ILE* 4.4 6.3 - - + -
165A ARG* 4.0 5.4 - - - +
172A LEU* 4.2 0.9 - - - -
173A ILE* 3.2 12.3 - - + +
175A ILE* 4.0 22.9 - - + +
188A LEU 4.5 2.9 + - - -
190A ILE* 3.0 36.5 + - + +
191A GLU 3.4 15.3 - - - +
192A ASN* 1.3 79.8 - - - +
194A VAL* 1.3 68.5 + - - +
195A GLN* 5.4 0.3 - - - +
252A GLY 4.8 2.3 + - - +
253A ILE* 3.9 18.2 - - - +
254A GLU* 3.5 18.5 + - - +
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Residues in contact with VAL 194 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A TRP* 4.6 11.2 - - + -
172A LEU* 3.9 13.7 - - + -
173A ILE 3.0 5.3 + - - -
174A ILE* 3.2 31.4 - - + -
175A ILE* 2.7 34.3 + - - +
193A THR* 1.3 79.0 - - - +
195A GLN* 1.3 71.3 + - - +
254A GLU* 3.4 29.4 - - + +
255A VAL 4.1 0.9 - - - +
256A PHE* 3.7 24.9 - - + -
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Residues in contact with GLN 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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175A ILE* 3.1 21.5 - - + +
177A GLY* 5.1 0.4 - - - +
184A PRO* 3.8 2.8 - - - +
185A VAL* 2.8 60.3 + - - +
188A LEU* 4.0 14.8 + - - +
193A THR* 5.4 0.6 + - - +
194A VAL* 1.3 76.6 - - - +
196A SER* 1.3 60.3 + - - +
197A CYS 4.0 0.5 + - - -
245A TRP* 3.8 9.6 - - + -
248A LEU* 3.2 26.0 - - + +
253A ILE* 3.8 24.9 - - + +
254A GLU 2.9 8.8 + - - +
255A VAL* 3.4 5.0 - - - -
256A PHE 3.1 23.0 + - - -
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Residues in contact with SER 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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42A ARG* 5.5 1.7 + - - -
135A ASN* 5.6 0.4 - - - -
174A ILE* 3.7 18.7 - - - +
175A ILE 2.8 8.4 + - - -
176A ASP* 3.4 22.7 + - - -
177A GLY 3.0 22.9 + - - -
181A GLY* 3.7 4.7 - - - +
195A GLN* 1.3 72.9 - - - +
197A CYS* 1.3 59.1 + - - +
198A ARG* 3.2 10.9 + - - -
245A TRP* 3.6 3.9 - - - -
256A PHE* 3.1 8.6 - - - -
258A GLY* 3.2 26.9 + - - -
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Residues in contact with CYS 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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181A GLY 3.2 10.8 - - - -
195A GLN 4.0 1.0 + - - -
196A SER* 1.3 71.0 - - - +
198A ARG* 1.3 78.1 + - - +
242A TYR* 3.8 24.2 - - + -
245A TRP* 3.3 37.6 - - + +
255A VAL* 4.3 12.3 - - - -
256A PHE 2.8 21.1 + - - -
257A CYS* 3.7 17.3 - - - -
258A GLY 3.2 13.0 + - - -
287A ILE* 4.5 3.8 - - - -
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Residues in contact with ARG 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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42A ARG* 3.3 8.1 - - - +
138A ASN* 3.0 20.2 + - - -
139A GLU* 2.9 22.2 + - - +
176A ASP* 2.8 29.8 + - - -
180A TYR 3.4 20.6 - - - +
181A GLY* 3.0 14.9 + - - +
182A ASN* 3.6 22.5 + - - +
196A SER* 3.2 20.6 + - - -
197A CYS* 1.3 91.7 + - - +
199A GLY* 1.3 54.2 + - - +
200A TYR* 3.7 17.1 + - + +
201A ILE* 5.0 0.5 - - - +
242A TYR* 2.6 30.3 + - - -
257A CYS* 3.4 5.8 - - - -
258A GLY* 4.0 1.2 - - - -
259A GLU* 3.2 42.2 + - - +
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Residues in contact with GLY 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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198A ARG* 1.3 71.7 - - - +
200A TYR* 1.3 60.8 + - - +
201A ILE 3.7 1.6 - - - -
242A TYR* 3.6 9.4 - - - -
257A CYS* 3.3 8.8 - - - -
259A GLU 2.8 15.9 + - - -
260A MSE 3.5 8.5 - - - +
261A GLY 3.2 21.8 + - - -
274A TRP* 3.3 16.6 - - - -
278A LEU* 4.0 9.2 - - - -
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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