Contacts of the strand formed by residues 194 - 199 (chain C) in PDB entry 3NIG
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 LEU 194 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146C CYS* 4.3 5.4 - - - -
164C LYS* 3.9 16.8 - - + -
167C CYS* 3.9 8.1 - - - -
185C ALA* 2.9 47.5 + - + +
188C GLY* 3.7 22.7 - - - -
189C TYR* 3.5 39.5 - - + +
193C GLY* 1.3 73.5 - - - +
195C LEU* 1.3 76.9 + - - +
196C ALA* 4.3 4.3 - - + +
221C LEU* 4.4 10.8 - - + -
222C SER* 3.0 19.3 - - - +
235C TRP* 3.4 11.0 + - - +
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Residues in contact with LEU 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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182C VAL* 4.0 22.9 - - + -
183C LEU 3.2 13.0 - - - +
184C GLY* 4.0 4.0 - - - -
194C LEU* 1.3 87.2 - - - +
196C ALA* 1.3 60.0 + - - +
221C LEU* 3.5 2.6 - - - -
222C SER* 2.9 30.7 + - - -
235C TRP* 3.4 16.2 - - + -
236C GLY* 3.9 22.2 - - - -
239C VAL* 4.3 8.7 - - + -
253C TYR* 4.3 9.6 - - + -
255C VAL* 3.3 30.7 - - + -
270C LEU* 4.6 0.9 - - + -
274C TYR* 3.7 27.3 + - + +
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Residues in contact with ALA 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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143C TYR* 4.3 4.2 - - + +
145C PRO* 3.6 28.9 - - + -
169C ALA* 6.0 1.1 - - + -
181C LEU 3.7 1.2 - - - +
182C VAL* 3.4 1.7 - - - +
183C LEU* 2.7 40.5 + - + +
185C ALA* 6.1 0.4 - - + -
194C LEU* 4.3 6.9 - - + +
195C LEU* 1.3 76.5 - - - +
197C GLN* 1.3 62.1 + - - +
220C SER 3.7 4.5 - - - -
221C LEU* 3.6 20.4 - - + -
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Residues in contact with GLN 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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143C TYR* 4.0 3.3 + - - -
180C GLU* 3.5 26.0 - - + +
181C LEU 3.1 13.2 - - - +
182C VAL* 3.8 14.6 - - + -
196C ALA* 1.3 76.6 - - - +
198C ALA* 1.3 83.6 + - - +
199C PRO* 3.5 5.9 - - - +
218C SER 4.2 6.5 + - - +
219C GLN* 3.1 5.4 - - - +
220C SER* 2.9 52.6 + - - +
253C TYR* 3.6 22.1 + - + +
272C SER 5.5 2.0 + - - -
274C TYR* 3.4 14.8 - - - +
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Residues in contact with ALA 198 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143C TYR* 3.4 27.6 + - + +
181C LEU* 3.0 29.2 + - - +
197C GLN* 1.3 81.8 + - - +
199C PRO* 1.3 74.0 - - + +
200C VAL 3.5 0.3 + - - -
203C ILE* 3.9 9.6 - - + +
216C VAL* 3.9 13.2 - - + -
219C GLN* 3.9 11.9 - - + +
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Residues in contact with PRO 199 (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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179C GLY 3.7 9.6 - - - +
180C GLU* 4.1 11.9 - - + +
197C GLN* 3.5 9.9 - - - +
198C ALA* 1.3 86.2 - - + +
200C VAL* 1.3 65.3 + - - +
201C ALA* 4.5 3.6 - - + +
202C ASP* 3.0 37.3 + - + +
203C ILE* 3.0 13.4 + - - +
218C SER* 3.5 28.7 - - - +
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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