Contacts of the strand formed by residues 194 - 203 (chain A) in PDB entry 5O67
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 GLU 194 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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178A THR* 3.5 27.6 - - + +
179A TYR 3.7 2.7 - - - -
180A GLN* 3.1 23.7 - - + +
193A SER* 1.3 77.3 - - - +
195A GLU* 1.3 66.5 + - - +
196A SER* 5.8 0.7 - - - +
253A TYR* 2.9 5.7 + - - -
344C LYS* 3.2 24.5 + - - -
358C VAL* 3.1 33.0 - - + +
361C ASP* 4.6 7.7 - - - +
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Residues in contact with GLU 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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178A THR* 3.6 2.8 - - - -
179A TYR* 3.0 35.8 + - - +
194A GLU* 1.3 78.6 - - - +
196A SER* 1.3 94.9 + - - +
253A TYR* 3.5 26.8 - - + -
254A VAL* 4.2 24.2 - - + -
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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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176A GLU* 6.0 4.3 - - - -
177A SER 3.4 9.0 - - - -
178A THR* 3.5 16.5 + - - +
194A GLU* 5.8 0.9 - - - +
195A GLU* 1.3 97.0 + - - +
197A VAL* 1.3 71.9 + - - +
198A SER* 6.1 0.4 - - - -
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Residues in contact with VAL 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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176A GLU* 3.8 0.3 - - - +
177A SER 3.1 29.1 + - - +
179A TYR* 4.4 16.4 - - + -
195A GLU 4.3 0.2 + - - -
196A SER* 1.3 81.4 - - - +
198A SER* 1.3 68.7 + - - +
254A VAL* 3.6 19.3 - - + -
255A PRO* 3.4 27.4 - - + +
256A GLU 4.3 4.7 - - - +
257A SER* 4.2 13.5 - - - -
258A LEU* 3.8 29.1 - - + +
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Residues in contact with SER 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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174A TYR* 5.4 5.6 - - - -
175A ARG 3.4 14.4 - - - -
176A GLU* 4.1 12.8 - - - -
196A SER* 6.1 0.7 - - - -
197A VAL* 1.3 84.0 - - - +
199A ARG* 1.3 66.2 + - - +
200A ASP* 4.4 10.2 + - - -
256A GLU 5.6 0.2 - - - +
257A SER* 5.1 3.3 - - - -
258A LEU* 4.2 8.9 + - - +
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Residues in contact with ARG 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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173A VAL 4.1 10.3 - - - +
174A TYR* 3.5 8.4 - - - -
175A ARG* 3.1 38.1 + - + +
198A SER* 1.3 81.9 + - - +
200A ASP* 1.3 66.4 + - - +
202A THR* 3.3 27.4 + - - +
236A LYS* 3.8 35.8 - - - +
241A ILE* 5.9 0.2 - - - +
257A SER* 3.8 23.9 + - - -
258A LEU* 3.1 33.3 + - + +
260A THR* 4.2 15.7 - - + +
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Residues in contact with ASP 200 (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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173A VAL 3.9 0.3 - - - +
174A TYR* 4.2 9.9 - - - -
198A SER* 4.4 9.6 + - - -
199A ARG* 1.3 82.4 + - - +
201A PRO* 1.3 67.5 - - + +
202A THR* 2.8 27.0 + - - -
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Residues in contact with PRO 201 (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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172A VAL* 4.1 18.1 - - + +
173A VAL 3.8 9.0 - - - +
174A TYR* 4.1 23.3 - - + -
200A ASP* 1.3 84.6 - - + +
202A THR* 1.3 59.1 + - - +
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Residues in contact with THR 202 (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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172A VAL* 3.4 7.0 - - - -
173A VAL* 2.7 32.3 + - - +
199A ARG* 3.3 22.0 + - - +
200A ASP 2.8 16.4 + - - -
201A PRO* 1.3 71.9 + - - +
203A ILE* 1.3 83.2 + - + +
236A LYS* 4.1 25.8 - - + -
260A THR* 4.6 3.1 - - - -
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Residues in contact with ILE 203 (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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170A VAL* 4.0 19.5 - - + -
171A PRO 3.5 13.2 - - - +
172A VAL* 5.1 6.5 - - + -
202A THR* 1.3 95.3 - - + +
204A GLY* 1.3 60.3 + - - +
206A VAL* 4.8 7.0 - - + -
234A THR* 3.9 31.2 - - - +
235A GLY* 4.0 3.0 - - - -
236A LYS* 4.8 0.5 + - - +
260A THR* 3.1 15.2 + - - -
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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