Contacts of the helix formed by residues 195 - 206 (chain C) in PDB entry 6Q2J
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 ASP 195 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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130C SER* 5.3 1.0 + - - -
192C ALA* 3.4 22.0 + - + +
193C GLN 3.3 1.2 - - - -
194C SER* 1.3 76.8 + - - +
196C ILE* 1.3 62.6 + - - +
197C PRO* 3.3 19.1 - - - +
198C CYS* 3.7 23.8 - - - +
199C GLN* 3.3 23.0 + - - +
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Residues in contact with ILE 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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290A THR 5.7 5.2 - - - +
193C GLN 5.8 0.2 - - - +
194C SER 3.0 11.4 + - - +
195C ASP* 1.3 71.2 + - - +
197C PRO* 1.4 70.4 - - + +
199C GLN* 3.5 18.3 + - + +
200C GLN* 2.9 38.6 + - + +
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Residues in contact with PRO 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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291A GLY* 5.6 2.9 - - - -
292A VAL* 3.7 35.4 - - + +
132C LEU* 4.8 17.5 - - + -
195C ASP* 3.3 17.0 - - - +
196C ILE* 1.4 97.9 - - + +
198C CYS* 1.3 57.4 + - - +
200C GLN* 3.2 7.1 + - + +
201C SER* 2.9 28.2 + - - -
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Residues in contact with CYS 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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130C SER* 3.3 15.5 - - - +
131C CYS* 4.1 1.9 - - - +
132C LEU* 3.7 22.4 - - + +
191C CYS* 2.0 50.3 - - - -
195C ASP* 3.7 28.0 - - - +
197C PRO* 1.3 77.5 - - - +
199C GLN* 1.3 62.6 + - - +
201C SER* 3.1 10.0 + - - -
202C LYS* 2.9 29.5 + - - +
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Residues in contact with GLN 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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191C CYS* 4.3 9.4 - - + -
192C ALA 5.1 0.4 - - - -
193C GLN* 3.0 53.1 + - - +
195C ASP 3.3 15.9 + - - +
196C ILE* 3.5 19.7 + - + +
197C PRO 3.3 0.4 - - - -
198C CYS* 1.3 86.0 - - - +
200C GLN* 1.3 57.1 + - - +
202C LYS* 3.5 23.8 + - - +
203C GLU* 2.8 33.0 + - - +
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Residues in contact with GLN 200 (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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290A THR* 5.0 10.8 - - - +
291A GLY* 5.9 0.7 - - - -
292A VAL 3.4 26.9 - - - +
293A SER* 6.0 0.4 - - - -
196C ILE* 2.9 30.7 + - + +
197C PRO* 3.5 7.6 - - + +
198C CYS 3.2 0.2 - - - -
199C GLN* 1.3 76.1 - - - +
201C SER* 1.3 60.2 + - - +
203C GLU* 2.9 28.0 + - - +
204C ALA* 4.0 6.2 + - - +
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Residues in contact with SER 201 (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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285A ILE* 6.4 0.2 - - - -
292A VAL* 4.6 10.7 + - - -
293A SER* 6.2 0.2 - - - +
294A LEU* 4.3 17.9 - - - -
131C CYS 4.2 3.5 + - - -
132C LEU* 4.1 23.1 + - - +
135C ALA* 5.0 7.4 - - - -
197C PRO 2.9 14.8 + - - -
198C CYS* 3.1 17.0 + - - -
200C GLN* 1.3 72.8 - - - +
202C LYS* 1.3 59.6 + - - +
203C GLU 3.3 0.2 - - - -
204C ALA* 3.0 10.1 + - - +
205C LEU* 2.9 31.3 + - - +
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Residues in contact with LYS 202 (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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131C CYS* 3.7 30.3 - - - -
189C CYS 4.6 7.4 - - - +
190C ASP* 4.8 14.6 + - - +
191C CYS* 5.0 11.7 + - - +
198C CYS 2.9 17.8 + - - +
199C GLN* 3.5 22.9 - - - +
200C GLN 3.2 0.2 - - - -
201C SER* 1.3 78.4 + - - +
203C GLU* 1.3 61.7 + - - +
205C LEU* 4.6 1.1 - - - +
206C HIS* 3.3 37.1 + - + +
208C LYS* 3.7 23.3 - - + +
313C ARG* 5.3 4.1 - - - +
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Residues in contact with GLU 203 (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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199C GLN* 2.8 36.3 + - - +
200C GLN* 2.9 28.5 + - - +
201C SER 3.3 0.4 - - - -
202C LYS* 1.3 79.0 - - - +
204C ALA* 1.3 57.4 + - - +
207C SER* 3.4 5.4 - - - -
208C LYS* 3.1 52.9 + - + +
209C THR* 4.4 18.0 + - + +
213C ASN* 5.8 0.2 - - - +
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Residues in contact with ALA 204 (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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293A SER* 5.9 1.1 - - - -
294A LEU* 3.9 34.8 - - + +
151C TYR* 4.5 0.9 - - - -
152C LEU* 3.8 22.6 - - + +
200C GLN 4.0 3.1 + - - +
201C SER* 3.0 14.5 + - - +
203C GLU* 1.3 78.9 - - - +
205C LEU* 1.3 66.1 + - - +
207C SER* 3.6 7.5 + - - -
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Residues in contact with LEU 205 (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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294A LEU* 4.1 18.2 - - + -
131C CYS* 3.4 33.9 - - + +
134C VAL* 4.1 13.9 - - + -
135C ALA* 3.7 31.2 - - + +
138C CYS* 5.8 2.0 - - + -
148C LEU* 4.8 17.8 - - + +
151C TYR* 3.3 21.5 + - - -
174C PHE* 6.1 0.3 - - - -
175C TYR* 5.6 0.3 + - - -
186C LEU* 4.6 29.6 - - + +
189C CYS* 5.1 2.2 - - - -
201C SER* 2.9 18.7 + - - +
202C LYS* 5.0 0.2 - - - -
204C ALA* 1.3 77.2 - - - +
206C HIS* 1.3 68.2 + - + +
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Residues in contact with HIS 206 (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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131C CYS* 4.2 0.4 - - - -
151C TYR* 3.7 4.4 + - - -
175C TYR* 5.0 9.2 - - - -
186C LEU* 3.3 21.4 + - + -
187C ALA* 4.2 12.6 + - - -
189C CYS* 3.6 34.1 - - - -
202C LYS* 3.3 33.0 + - + +
205C LEU* 1.3 81.0 - - + +
207C SER* 1.3 73.2 + - - +
208C LYS* 3.8 15.5 - - + -
211C ALA* 4.5 0.2 - - - +
212C VAL* 4.1 4.0 - - + +
283C LEU* 6.2 2.9 - - + -
288C GLN* 3.7 27.3 + - - +
313C ARG* 4.2 8.7 + - - -
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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