Contacts of the helix formed by residues 189 - 198 (chain B) in PDB entry 6C1A
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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187B PHE* 4.8 0.2 - - - +
188B ARG* 1.3 81.6 + - - +
190B LYS* 1.3 59.3 + - - +
191B PRO* 3.5 5.4 - - - +
192B GLN* 3.1 20.6 + - - +
193B LEU* 3.0 24.1 + - - +
208B PHE* 3.2 18.6 - - - -
10D C 3.7 26.2 - - - -
11D C 2.6 28.5 + - - -
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Residues in contact with LYS 190 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189B SER* 1.3 69.6 - - - +
191B PRO* 1.4 70.3 - - + +
193B LEU* 3.3 3.9 + - + +
194B ALA* 2.8 29.6 + - + +
203B LEU* 2.8 39.2 + - + -
204B SER* 3.5 13.9 + - - +
205B SER 4.5 0.2 - - - -
206B PHE* 2.5 38.9 + - + +
208B PHE* 3.4 30.2 - - + +
10D C 3.4 10.5 + - - +
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Residues in contact with PRO 191 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189B SER* 3.5 11.9 - - - +
190B LYS* 1.4 89.4 - - + +
192B GLN* 1.3 55.4 + - - +
194B ALA* 3.3 7.8 + - + +
195B ARG* 3.0 45.1 + - - +
10D C 3.3 32.3 - - - +
11D C 4.6 10.1 - - - +
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Residues in contact with GLN 192 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186B LYS 3.5 19.4 + - - -
187B PHE* 3.6 25.6 - - + -
188B ARG* 3.0 31.1 + - - +
189B SER* 3.1 21.6 + - - +
191B PRO* 1.3 76.5 - - - +
193B LEU* 1.3 62.6 + - - +
195B ARG* 3.4 27.6 + - - +
196B TYR* 3.3 16.6 + - - +
11D C 4.2 6.4 + - - +
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Residues in contact with LEU 193 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155B LEU* 4.6 6.1 - - + -
159B TRP* 3.7 38.6 - - + -
179B TYR* 4.2 9.6 - - + -
187B PHE* 3.9 18.1 - - + -
189B SER 3.0 16.5 + - - +
190B LYS* 3.3 4.7 + - - +
192B GLN* 1.3 74.4 - - - +
194B ALA* 1.3 65.7 + - - +
196B TYR* 3.4 1.9 + - - +
197B LEU* 3.2 31.6 + - + +
203B LEU* 4.0 13.9 - - + -
206B PHE* 3.8 32.1 - - + -
208B PHE* 4.0 17.3 - - + -
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Residues in contact with ALA 194 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190B LYS* 2.8 19.7 + - + +
191B PRO* 3.3 9.2 + - + +
193B LEU* 1.3 78.5 - - - +
195B ARG* 1.3 51.6 + - - +
197B LEU* 5.0 0.4 - - - -
198B GLY* 2.8 35.2 + - - +
203B LEU* 3.7 22.9 - - + +
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Residues in contact with ARG 195 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191B PRO* 3.0 33.9 + - - +
192B GLN* 3.8 27.1 - - - +
193B LEU 3.2 0.4 - - - -
194B ALA* 1.3 76.3 - - - +
196B TYR* 1.3 64.5 + - - +
197B LEU 3.6 0.2 + - - -
198B GLY* 3.7 7.8 + - - -
11D C 4.9 10.1 + - - -
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Residues in contact with TYR 196 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159B TRP* 4.2 15.3 - + + -
181B SER* 4.2 15.3 - - - -
182B PRO* 5.9 0.2 - - + -
183B SER* 5.2 1.0 - - - -
185B LYS* 5.3 4.9 - - + -
187B PHE* 3.4 40.8 - + + -
192B GLN 3.3 5.5 + - - +
193B LEU 3.4 3.5 + - - +
195B ARG* 1.3 80.0 - - - +
197B LEU* 1.3 66.5 + - + +
305B UNX 3.0 26.5 - - - -
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Residues in contact with LEU 197 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155B LEU* 4.8 9.0 - - + -
156B PRO* 5.3 3.6 - - + -
159B TRP* 4.1 32.1 - - + +
193B LEU* 3.2 36.9 + - + +
194B ALA 4.3 1.3 - - - +
196B TYR* 1.3 85.8 - - + +
198B GLY* 1.3 62.7 + - - +
200B THR* 2.7 44.1 + - - +
201B VAL* 4.1 31.2 - - + +
203B LEU* 4.4 10.8 - - + -
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Residues in contact with GLY 198 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194B ALA* 2.8 24.1 + - - +
195B ARG* 3.7 6.2 + - - -
196B TYR 3.6 2.2 - - - -
197B LEU* 1.3 72.4 - - - +
199B ASN* 1.3 61.3 + - - -
200B THR 3.2 4.7 + - - -
201B VAL 3.3 18.2 - - - +
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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