Contacts of the strand formed by residues 192 - 198 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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118C LEU* 4.1 2.4 - - - +
133C LEU* 3.5 24.5 - - + -
149C TRP* 5.5 1.1 - + + -
150C LYS 3.2 15.5 - - - -
151C ALA* 3.3 26.3 - - + +
156C VAL* 4.6 3.8 - - + -
179C LEU* 4.2 17.7 - - + -
181C LEU* 3.4 32.5 - - + +
185C GLN* 3.5 24.0 + - - +
186C TRP* 3.3 31.2 - + - -
189C HIS* 4.0 18.4 - - + -
191C SER* 1.3 81.6 - - - +
193C SER* 1.3 61.1 + - - +
205C LYS 4.0 0.5 - - - +
206C THR* 3.2 5.6 - - - +
207C VAL* 2.9 44.0 + - + +
209C PRO* 5.9 0.2 - - + -
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Residues in contact with SER 193 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148C ALA 3.9 0.3 - - - +
149C TRP* 3.4 13.5 - - - -
150C LYS* 3.1 58.0 + - - +
152C ASP 4.9 2.0 + - - -
191C SER* 4.5 3.0 + - - -
192C TYR* 1.3 74.1 - - - +
194C CYS* 1.3 59.9 + - - +
195C GLN* 4.0 4.3 - - - +
204C GLU* 3.3 28.5 + - - -
205C LYS 3.4 7.4 - - - -
206C THR* 3.9 9.2 - - - +
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Residues in contact with CYS 194 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116C VAL* 5.0 1.2 - - - +
118C LEU* 3.7 20.2 - - + +
135C CYS* 2.0 54.7 - - + -
147C VAL* 4.8 4.0 - - - -
148C ALA 3.9 2.9 - - - -
149C TRP* 4.2 19.5 - - + -
193C SER* 1.3 72.7 - - - +
195C GLN* 1.3 61.4 + - - +
196C VAL* 4.0 10.2 + - - +
203C VAL 4.3 0.3 - - - +
204C GLU* 4.0 1.8 - - - -
205C LYS* 2.9 27.9 + - + +
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Residues in contact with GLN 195 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147C VAL* 3.2 6.1 - - - +
148C ALA* 2.9 41.2 + - + +
150C LYS* 3.4 40.9 + - - +
193C SER* 4.5 4.3 - - - +
194C CYS* 1.3 72.1 - - - +
196C VAL* 1.3 63.6 + - - +
197C THR* 4.3 1.1 + - - -
202C THR* 4.3 10.9 - - + +
203C VAL 3.6 9.6 - - - +
204C GLU* 3.5 36.8 + - + +
213K ILE* 3.4 29.7 - - + +
214K PRO* 4.9 4.0 + - - +
216K HIS* 5.9 1.6 + - - -
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Residues in contact with VAL 196 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114C PRO* 4.0 18.1 - - + +
116C VAL* 3.6 27.4 - - + -
137C ILE* 3.6 32.5 - - + -
145C VAL* 4.3 6.5 - - + -
146C THR 3.2 9.2 - - - +
147C VAL* 3.9 7.2 - - + -
194C CYS* 4.0 16.6 + - - +
195C GLN* 1.3 78.2 - - - +
197C THR* 1.3 61.4 + - - +
198C HIS 4.1 0.2 + - - -
201C SER 3.7 1.6 - - - +
202C THR* 3.5 3.2 - - - -
203C VAL* 3.1 36.4 + - + +
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Residues in contact with THR 197 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145C VAL* 3.1 9.6 - - - +
146C THR* 3.0 44.2 + - - -
195C GLN 5.4 0.5 - - - -
196C VAL* 1.3 72.9 - - - +
198C HIS* 1.3 63.6 + - - +
200C GLY* 3.9 17.0 - - - +
201C SER 3.5 2.0 - - - -
202C THR* 3.8 14.3 + - - +
211K GLU* 3.6 33.0 + - + +
212K PRO 6.4 0.2 - - - -
213K ILE* 3.2 29.0 - - + +
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Residues in contact with HIS 198 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111C LYS* 5.0 6.9 + - + +
112C ALA 3.2 22.1 + - - -
113C ALA* 4.3 1.1 - - - -
114C PRO* 3.4 39.2 - - + +
140C PHE* 3.5 20.3 - + + +
141C TYR 3.4 7.0 + - - -
142C PRO* 3.5 30.0 + - + -
144C ALA 3.6 15.1 + - - -
145C VAL* 4.3 4.0 - - + -
197C THR* 1.3 77.2 - - - +
199C GLU* 1.3 91.4 + - + +
201C SER* 3.0 25.2 + - - +
211K GLU* 5.3 0.2 - - - -
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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