Contacts of the strand formed by residues 194 - 199 (chain A) in PDB entry 3G65
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 194 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179A ARG* 3.6 44.6 - - + +
180A SER 4.0 9.6 - - - +
182A HIS* 4.2 17.0 - - - +
192A ALA 3.5 9.8 + - - +
193A MET* 1.3 75.0 - - - +
195A THR* 1.3 61.6 + - - +
196A GLU* 3.9 2.3 + - + +
110C PHE* 5.4 8.3 - - + -
130C THR 3.6 4.0 - - - +
132C ASP* 3.2 43.6 + - + +
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Residues in contact with THR 195 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158A PRO* 3.7 24.9 + - + +
159A PHE* 3.3 19.5 - - + -
160A SER 5.6 0.3 + - - -
179A ARG* 3.4 1.6 - - - +
180A SER* 2.8 45.6 + - - -
193A MET* 3.7 12.7 + - - +
194A VAL* 1.3 72.6 - - - +
196A GLU* 1.3 63.9 + - - +
90C ARG* 4.9 4.7 + - - -
129C VAL* 4.2 3.6 - - + -
130C THR 3.6 3.6 - - - -
131C HIS* 3.2 37.5 + - + -
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Residues in contact with GLU 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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177A ILE* 3.4 40.1 - - + +
178A LEU 3.2 4.5 - - - +
179A ARG* 3.3 38.1 + - + +
194A VAL* 4.9 2.7 - - + +
195A THR* 1.3 78.8 - - - +
197A MET* 1.3 60.4 + - - +
198A CYS* 5.3 3.9 - - + +
128C ILE 3.7 1.4 - - - +
129C VAL* 3.5 3.0 - - - -
130C THR* 2.9 54.0 + - + +
132C ASP* 6.2 0.2 - - - +
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Residues in contact with MET 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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154A GLU 3.5 20.0 - - - +
155A ALA* 3.4 35.2 - - + +
158A PRO* 3.4 22.9 - - + -
159A PHE* 4.2 6.0 - - + -
176A VAL 4.0 0.3 - - - +
177A ILE* 3.3 6.4 - - - +
178A LEU* 2.8 46.7 + - + +
195A THR* 4.9 0.2 - - - +
196A GLU* 1.3 73.2 - - - +
198A CYS* 1.3 75.5 + - - +
199A LEU* 4.1 16.3 - - + +
119C LEU* 4.5 9.9 - - + -
127C ARG* 4.8 6.1 - - + +
128C ILE 3.6 7.2 - - - +
129C VAL* 3.4 30.5 - - + +
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Residues in contact with CYS 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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175A ARG* 3.1 44.6 - - - -
176A VAL 3.6 4.9 - - - -
177A ILE* 4.2 11.7 - - + -
196A GLU* 5.3 4.0 - - + +
197A MET* 1.3 75.9 - - - +
199A LEU* 1.3 72.0 + - - +
126C SER 4.4 3.3 - - - +
127C ARG* 4.0 2.9 - - - -
128C ILE* 2.8 50.9 + - + +
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Residues in contact with LEU 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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151A VAL* 4.2 17.0 - - + +
152A LEU* 5.3 2.0 - - + -
154A GLU 6.2 0.2 - - - -
155A ALA* 3.5 30.3 - - + -
175A ARG* 3.1 23.2 - - - +
176A VAL* 2.9 38.1 + - + -
178A LEU* 5.8 1.3 - - + -
197A MET* 4.1 17.5 - - + -
198A CYS* 1.3 81.6 - - - +
200A GLY* 1.3 60.7 + - - +
203A ASP* 3.5 17.7 - - - +
204A PHE* 4.1 16.4 - - + -
127C ARG* 3.6 26.9 - - - +
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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