Contacts of the strand formed by residues 192 - 198 (chain M) in PDB entry 4R2G
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 TYR 192 (chain M).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118M LEU* 4.3 3.4 - - - +
133M LEU* 3.5 21.8 - - + -
149M TRP* 5.0 1.8 - + + -
150M LYS 3.3 17.5 - - - -
151M ALA* 3.8 20.0 - - + +
152M ASP 4.6 0.4 - - - +
156M VAL* 4.6 2.9 - - + -
179M LEU* 3.6 23.6 - - + -
181M LEU* 3.5 29.8 - - + +
185M GLN* 3.0 25.0 + - - +
186M TRP* 3.6 27.4 - + + -
189M HIS* 3.5 29.4 + + + -
191M SER* 1.3 79.9 - - - +
193M SER* 1.3 64.2 + - - +
206M THR* 3.3 3.0 - - - +
207M VAL* 3.0 34.9 + - - +
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Residues in contact with SER 193 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118M LEU* 4.4 0.2 - - - -
148M ALA 3.7 0.7 - - - +
149M TRP* 3.4 13.5 - - - -
150M LYS* 3.0 49.1 + - - +
152M ASP 4.3 3.1 + - - -
191M SER* 4.3 4.5 + - - -
192M TYR* 1.3 76.0 - - - +
194M CYS* 1.3 60.0 + - - +
195M GLN* 4.0 1.6 - - - -
204M GLU* 3.8 19.1 + - - -
205M LYS 3.2 5.2 - - - -
206M THR* 2.8 25.6 + - - +
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Residues in contact with CYS 194 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116M VAL* 4.9 0.9 - - - +
118M LEU* 3.5 20.9 - - + +
135M CYS* 2.1 54.4 - - + -
147M VAL* 4.0 12.8 - - - -
148M ALA 3.9 1.6 - - - -
149M TRP* 3.7 20.0 - - + -
193M SER* 1.3 72.8 - - - +
195M GLN* 1.3 61.1 + - - +
196M VAL* 4.1 4.5 + - - +
203M VAL 4.3 0.5 - - - +
204M GLU* 3.7 0.9 - - - -
205M LYS* 2.8 33.6 + - - +
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Residues in contact with GLN 195 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213E ILE* 4.4 17.1 - - + +
214E PRO* 4.3 7.8 + - - +
146M THR 3.6 0.5 - - - +
147M VAL* 3.4 4.0 - - - +
148M ALA* 2.8 54.3 + - + +
150M LYS* 3.2 42.8 + - + +
193M SER* 4.6 1.3 - - - -
194M CYS* 1.3 72.1 - - - +
196M VAL* 1.3 63.7 + - - +
202M THR* 3.9 15.0 - - - +
203M VAL 3.8 3.4 - - - +
204M GLU* 3.6 41.5 + - + +
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Residues in contact with VAL 196 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114M PRO* 3.9 23.8 - - + -
116M VAL* 3.6 38.4 - - + -
135M CYS* 4.5 4.5 - - - -
137M ILE* 4.0 13.9 - - + -
145M VAL* 3.7 22.7 - - + -
146M THR 3.1 8.5 - - - +
147M VAL* 4.5 5.6 - - + -
194M CYS* 4.4 3.1 - - - +
195M GLN* 1.3 79.3 - - - +
197M THR* 1.3 62.4 + - - +
198M HIS 4.3 0.2 + - - -
202M THR* 3.4 3.8 + - - -
203M VAL* 2.8 41.6 + - + +
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Residues in contact with THR 197 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211E GLU* 3.7 30.4 + - + +
212E PRO 5.8 2.0 - - - +
213E ILE* 3.2 18.3 - - + +
145M VAL* 3.5 5.5 - - - +
146M THR* 3.0 41.7 + - - -
196M VAL* 1.3 75.0 - - - +
198M HIS* 1.3 66.7 + - - +
200M GLY 3.2 31.9 - - - +
201M SER 4.1 0.7 - - - +
202M THR* 3.0 19.1 + - - +
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Residues in contact with HIS 198 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211E GLU* 5.3 0.2 - - - -
111M LYS* 4.1 6.3 - - + -
112M ALA 3.1 25.5 + - - -
113M ALA* 4.0 4.4 - - - +
114M PRO* 3.6 33.9 - - + +
140M PHE* 3.9 7.6 - + - -
141M TYR 3.1 29.5 + - - -
142M PRO* 3.4 11.6 + - + +
144M ALA 3.1 27.1 - - - +
145M VAL* 4.7 2.5 - - + +
196M VAL 4.3 0.4 + - - -
197M THR* 1.3 76.7 - - - +
199M GLU* 1.3 89.6 + - + +
200M GLY 3.2 0.7 - - - +
201M SER* 3.1 22.7 + - - +
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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