Contacts of the helix formed by residues 189 - 198 (chain F) in PDB entry 6C1V
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 SER 189 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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187F PHE* 4.8 0.5 - - - +
188F ARG* 1.3 79.0 + - - +
190F LYS* 1.3 58.5 + - - +
191F PRO* 3.6 4.9 - - - +
192F GLN* 3.3 19.6 + - - +
193F LEU* 3.0 27.4 + - - +
208F PHE* 3.4 10.6 - - - -
10H C 3.5 31.0 - - - -
11H C 2.6 29.3 + - - -
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Residues in contact with LYS 190 (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 SER* 1.3 68.9 - - - +
191F PRO* 1.4 69.6 - - + +
193F LEU* 3.6 3.8 - - + +
194F ALA* 2.8 30.4 + - + +
203F LEU* 2.8 35.8 + - + +
204F SER* 3.4 13.7 + - - +
205F SER 4.9 0.2 - - - -
206F PHE* 2.8 31.8 + - + +
208F PHE* 3.5 33.5 - - + +
10H C 3.4 9.8 + - - +
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Residues in contact with PRO 191 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189F SER* 3.6 11.0 - - - +
190F LYS* 1.4 90.2 - - + +
192F GLN* 1.3 51.3 + - - +
194F ALA* 3.0 8.5 + - + +
195F ARG* 2.9 36.0 + - - +
10H C 3.2 33.2 - - - +
11H C 5.1 7.2 - - - +
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Residues in contact with GLN 192 (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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186F LYS 4.2 11.7 + - - -
187F PHE* 3.8 22.2 - - + -
188F ARG* 3.2 28.9 + - - +
189F SER* 3.3 20.9 + - - +
191F PRO* 1.3 73.1 - - - +
193F LEU* 1.3 66.1 + - - +
195F ARG* 4.2 5.4 - - - +
196F TYR* 3.3 22.7 + - - +
11H C 4.6 7.6 + - - +
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Residues in contact with LEU 193 (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* 4.5 8.3 - - + -
159F TRP* 3.3 43.5 - - + -
179F TYR* 4.2 21.1 - - + -
187F PHE* 4.3 16.3 - - + -
189F SER 3.0 17.6 + - - +
190F LYS* 3.7 5.8 - - - +
192F GLN* 1.3 77.4 - - - +
194F ALA* 1.3 58.6 + - - +
196F TYR* 3.4 2.3 + - - +
197F LEU* 3.1 38.4 + - + +
203F LEU* 4.3 7.2 - - + -
206F PHE* 3.9 30.1 - - + -
208F PHE* 4.3 7.9 - - + -
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Residues in contact with ALA 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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190F LYS* 2.8 24.0 + - + +
191F PRO* 3.0 7.2 + - + +
193F LEU* 1.3 73.4 - - - +
195F ARG* 1.3 52.4 + - - +
197F LEU* 3.8 0.6 - - - +
198F GLY* 2.8 35.2 + - - +
203F LEU* 3.7 22.4 - - + +
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Residues in contact with ARG 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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191F PRO 2.9 19.1 + - - +
192F GLN* 4.2 6.1 - - - +
193F LEU 3.4 0.2 - - - -
194F ALA* 1.3 69.5 - - - +
196F TYR* 1.3 67.6 + - - +
198F GLY* 3.6 9.2 + - - -
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Residues in contact with TYR 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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159F TRP* 3.5 36.8 - + + -
181F SER* 4.0 7.1 + - - -
182F PRO* 5.6 0.2 - - + -
183F SER* 4.8 3.5 - - - -
185F LYS* 4.9 6.5 - - + +
187F PHE* 3.5 25.8 - + + -
192F GLN 3.3 15.2 + - - +
193F LEU 3.7 7.2 - - - +
195F ARG* 1.3 76.4 - - - +
197F LEU* 1.3 66.3 + - + +
198F GLY* 3.4 0.7 + - - -
301F UNX 2.9 25.9 - - - -
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Residues in contact with LEU 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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155F LEU* 4.1 26.0 - - + -
156F PRO* 4.5 5.8 - - + -
159F TRP* 3.7 36.6 - - + +
193F LEU* 3.1 27.7 + - + +
194F ALA 4.2 2.2 - - - +
196F TYR* 1.3 84.2 - - + +
198F GLY* 1.3 63.9 + - - +
200F THR* 3.4 22.0 - - - -
201F VAL* 3.9 28.7 - - + +
203F LEU* 4.2 19.1 - - + -
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Residues in contact with GLY 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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194F ALA 2.8 22.5 + - - +
195F ARG* 4.0 7.9 - - - -
196F TYR 3.4 3.3 - - - -
197F LEU* 1.3 70.2 - - - +
199F ASN* 1.3 57.7 + - - -
200F THR 3.1 7.5 + - - -
201F VAL 2.9 21.1 - - - +
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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