Contacts of the helix formed by residues 193 - 199 (chain F) in PDB entry 2NYM
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 GLY 193 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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173F SER* 5.2 1.3 - - - -
190F PRO* 5.2 2.0 - - - -
192F GLU* 1.3 76.7 - - - +
194F PRO* 1.3 76.1 - - - +
195F MET 3.4 1.6 - - - -
196F CYS* 3.1 4.8 + - - +
197F ASP* 2.6 34.3 + - - +
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Residues in contact with PRO 194 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171F SER* 4.1 7.8 + - - +
173F SER* 3.8 25.6 - - - +
174F ILE* 3.7 18.6 - - + -
183F LEU* 3.1 38.1 - - + -
193F GLY* 1.3 80.1 - - - +
195F MET* 1.3 75.4 + - + +
197F ASP* 2.6 22.2 + - - +
198F LEU* 3.1 9.7 + - - +
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Residues in contact with MET 195 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115F ARG* 4.6 2.7 - - - +
155F LEU* 3.7 26.2 - - + -
183F LEU* 3.8 14.5 - - + +
184F ASP 4.1 7.2 - - - +
185F ARG* 3.5 34.1 - - - +
187F GLN* 3.4 33.2 - - + +
188F GLU 3.4 3.8 - - - +
189F VAL* 3.5 13.9 - - + +
190F PRO* 3.3 33.9 - - + -
193F GLY* 5.1 0.4 - - - -
194F PRO* 1.3 85.0 - - + +
196F CYS* 1.3 67.0 + - - +
197F ASP 3.1 0.2 + - - -
198F LEU* 3.1 10.3 + - - +
199F LEU* 3.3 17.2 - - + +
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Residues in contact with CYS 196 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189F VAL* 4.2 11.4 - - - -
190F PRO* 3.0 32.3 - - + +
191F HIS 3.9 8.3 - - - -
192F GLU* 4.0 2.7 - - - -
193F GLY* 3.1 19.1 + - - +
194F PRO 3.1 0.2 - - - -
195F MET* 1.3 80.8 - - - +
197F ASP* 1.3 58.5 + - - +
199F LEU* 3.0 17.7 + - - +
200F TRP* 3.1 28.1 + - - -
216F ALA* 3.8 28.9 - - - -
217F GLY 4.3 5.6 - - - -
5H 1ZN 4.3 0.9 - - - -
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Residues in contact with ASP 197 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169F GLY 4.2 0.9 - - - -
171F SER* 2.9 37.2 + - - +
173F SER* 5.3 1.6 + - - -
192F GLU* 6.0 0.2 - - - -
193F GLY 2.6 29.6 + - - +
194F PRO* 2.6 8.7 + - - +
196F CYS* 1.3 68.7 - - - +
198F LEU* 1.3 60.8 + - - +
199F LEU 2.8 5.8 + - - -
200F TRP 4.2 1.6 - - - +
201F SER* 2.8 37.0 + - - +
217F GLY* 2.8 34.0 + - - -
218F TYR* 3.5 21.4 + - - -
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Residues in contact with LEU 198 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155F LEU* 3.9 25.1 - - + -
156F THR* 4.4 9.9 - - + -
164F PHE* 4.9 1.1 - - + -
166F LEU* 3.5 23.3 - - + +
167F HIS 4.3 0.3 + - - -
168F GLY* 2.8 23.8 + - - -
169F GLY 3.3 19.2 + - - +
170F LEU* 5.1 4.7 - - - -
171F SER* 5.1 2.2 - - - +
174F ILE* 3.5 32.5 - - + -
180F ILE* 3.9 31.4 - - + -
183F LEU* 4.4 2.7 - - + -
194F PRO 3.1 2.8 + - - +
195F MET 3.1 9.1 + - - +
197F ASP* 1.3 75.1 - - - +
199F LEU* 1.3 67.3 + - + +
228F PHE* 6.4 0.4 - - + -
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Residues in contact with LEU 199 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115F ARG* 3.6 47.6 - - + +
116F GLY 3.8 13.5 - - - +
117F ASN* 3.4 16.3 - - - +
155F LEU* 4.0 23.3 - - + +
167F HIS* 3.3 21.8 - - + +
168F GLY* 3.8 9.2 - - - +
189F VAL* 4.2 17.3 - - + -
195F MET* 3.3 16.6 - - + +
196F CYS 3.0 7.8 + - - +
197F ASP 2.9 0.8 - - - -
198F LEU* 1.3 93.3 - - + +
200F TRP* 1.3 64.6 + - + +
241F HIS* 3.9 1.7 + - - -
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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