Contacts of the helix formed by residues 196 - 211 (chain C) in PDB entry 6GL7
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 ASN 196 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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184C ILE* 5.0 5.8 + - + +
187C ARG* 4.4 0.6 + - - +
189C ILE* 3.4 22.4 - - + +
193C GLU* 4.8 5.8 + - - +
195C CYS* 1.3 70.6 - - - +
197C ARG* 1.3 58.6 + - - +
198C ARG* 3.2 17.6 + - - +
199C LYS* 3.0 54.8 + - + +
200C CYS* 2.9 26.2 + - - +
241C CYS* 4.6 0.2 - - - -
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Residues in contact with ARG 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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195C CYS* 3.4 13.2 + - - +
196C ASN* 1.3 73.1 + - - +
198C ARG* 1.3 53.1 + - - +
200C CYS* 3.3 6.7 - - - +
201C HIS* 2.7 59.1 + - + +
241C CYS 3.2 19.1 - - - +
242C SER 2.9 27.3 + - - -
243C TYR* 3.0 22.9 + - - +
244C GLU 4.3 1.8 - - - -
245C ASP* 3.1 38.2 + - - +
304C ASP* 5.3 7.1 + - - +
306C THR* 5.4 4.4 - - - -
322C TRP* 4.4 10.5 - - - +
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Residues in contact with ARG 198 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196C ASN* 3.2 11.5 + - - +
197C ARG* 1.3 78.7 - - - +
199C LYS* 1.3 85.7 + - - +
201C HIS* 3.2 10.0 + - + +
202C LYS* 2.9 42.6 + - - +
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Residues in contact with LYS 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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184C ILE* 3.9 18.7 - - + +
196C ASN* 3.0 41.6 + - + +
198C ARG* 1.3 95.2 - - - +
200C CYS* 1.3 60.5 + - - +
202C LYS* 3.3 12.3 + - + +
203C ALA* 2.9 29.8 + - - +
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Residues in contact with CYS 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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184C ILE* 3.9 6.5 - - - +
185C CYS* 2.0 52.7 - - + -
196C ASN 2.9 9.1 + - - +
197C ARG* 3.2 9.6 + - - +
199C LYS* 1.3 77.2 - - - +
201C HIS* 1.3 56.7 + - - +
203C ALA* 3.2 3.0 + - - +
204C LEU* 2.7 47.7 + - - +
241C CYS* 3.5 24.9 - - - -
242C SER* 3.7 12.3 - - - -
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Residues in contact with HIS 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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197C ARG* 2.7 51.0 + - + +
198C ARG* 3.2 8.2 + - - +
200C CYS* 1.3 72.1 - - - +
202C LYS* 1.3 53.2 + - - +
204C LEU* 3.2 4.6 + - + +
205C ARG* 2.7 40.5 + - - +
242C SER* 2.8 40.0 + - - -
302C GLY* 3.4 35.8 + - - +
303C PHE 3.9 19.1 + - - -
304C ASP* 5.1 5.4 + - - -
306C THR* 4.0 5.3 + - + -
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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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198C ARG* 2.9 28.8 + - - +
199C LYS* 3.5 14.1 - - + +
201C HIS* 1.3 75.3 - - - +
203C ALA* 1.3 61.1 + - - +
205C ARG* 3.2 18.5 + - - +
206C GLN* 3.0 35.2 + - + +
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Residues in contact with ALA 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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180C SER 4.3 1.1 - - - +
181C TYR* 3.4 31.9 - - + +
184C ILE* 3.8 17.7 - - + -
199C LYS 2.9 16.5 + - - +
200C CYS* 3.5 7.0 - - - +
202C LYS* 1.3 76.9 - - - +
204C LEU* 1.3 58.0 + - - +
206C GLN* 3.5 4.7 + - - +
207C PHE* 2.8 29.5 + - - +
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Residues in contact with LEU 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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181C TYR* 3.2 40.8 - - + -
185C CYS* 4.1 1.1 - - - -
200C CYS* 2.7 29.2 + - - +
201C HIS* 3.7 8.7 - - + +
203C ALA* 1.3 72.4 - - - +
205C ARG* 1.3 62.8 + - - +
207C PHE* 4.0 2.2 - - + -
208C PHE* 3.0 39.9 + - + +
237C ILE* 3.9 26.0 - - + +
242C SER* 3.3 36.8 - - - +
301C ILE* 4.2 19.1 - - + -
302C GLY* 4.9 0.9 - - - -
306C THR* 6.0 0.2 - - + -
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Residues in contact with ARG 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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102C GLU* 5.3 3.8 - - - -
201C HIS* 2.7 23.9 + - - +
202C LYS* 3.5 16.0 - - - +
204C LEU* 1.3 73.4 - - - +
206C GLN* 1.3 72.7 + - - +
208C PHE* 3.9 2.6 + - - +
209C ASP* 3.2 31.6 + - - +
263C LEU* 4.5 15.8 - - - +
267C ARG* 4.4 17.4 + - - +
301C ILE 4.2 13.6 + - - +
302C GLY* 2.9 23.8 + - - -
303C PHE* 3.6 35.6 - - + +
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Residues in contact with GLN 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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102C GLU* 5.4 4.9 + - - -
177C LEU* 6.0 1.1 - - + -
202C LYS* 3.0 28.4 + - + +
203C ALA* 4.0 4.7 - - - +
205C ARG* 1.3 89.4 + - - +
207C PHE* 1.3 64.9 + - - +
209C ASP* 3.1 7.5 + - - +
210C ARG* 2.8 74.1 + - - +
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Residues in contact with PHE 207 (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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174C CYS 4.3 1.1 - - - -
177C LEU* 3.5 17.0 - - + +
178C ARG* 3.3 29.4 - - + -
181C TYR* 3.4 35.9 - + + -
203C ALA 2.8 23.2 + - - +
204C LEU* 3.2 5.4 + - - +
206C GLN* 1.3 72.1 - - - +
208C PHE* 1.3 98.0 + + - +
210C ARG* 5.2 0.9 - - - -
211C VAL* 3.1 62.2 + - + +
216C THR* 4.7 3.4 - - + -
219C MET* 4.1 25.1 - - + -
236C THR* 6.0 1.8 - - + -
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Residues in contact with PHE 208 (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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97C ARG* 4.2 7.3 + - - +
181C TYR* 5.6 0.9 - - - -
204C LEU* 3.0 32.1 + - + +
205C ARG* 4.7 2.5 - - - +
207C PHE* 1.3 105.8 - + - +
209C ASP* 1.3 63.7 + - - +
211C VAL 4.8 1.6 - - - +
216C THR* 3.9 32.4 + - - +
217C TYR* 6.5 0.2 - + - -
220C LEU* 3.9 35.9 - - + -
236C THR* 4.6 4.9 - - + -
237C ILE* 3.5 33.9 - - + -
298C ALA* 5.0 15.8 - - + +
301C ILE* 3.7 27.1 - - + +
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Residues in contact with ASP 209 (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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97C ARG* 3.0 32.1 + - - +
98C GLY* 5.5 9.6 + - - -
102C GLU* 5.5 0.2 - - - +
205C ARG* 3.2 21.6 + - - +
206C GLN* 3.1 10.5 + - - +
208C PHE* 1.3 80.5 - - - +
210C ARG* 1.3 62.5 + - + +
211C VAL 3.6 4.2 - - - +
267C ARG* 3.3 27.2 + - - -
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Residues in contact with ARG 210 (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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177C LEU* 3.8 31.5 - - + +
206C GLN* 2.8 50.5 + - - +
209C ASP* 1.3 79.7 - - + +
211C VAL* 1.3 64.2 + - - +
212C PRO* 3.8 4.3 - - - +
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Residues in contact with VAL 211 (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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174C CYS* 3.7 15.9 - - + -
177C LEU* 3.4 25.1 - - + -
207C PHE* 3.1 44.9 + - + +
208C PHE 4.8 0.9 - - - +
209C ASP 4.5 4.3 - - - +
210C ARG* 1.3 79.6 + - - +
212C PRO* 1.3 87.9 - - + +
213C SER* 3.5 1.7 + - - -
215C TYR* 3.6 17.5 - - + -
216C THR* 3.5 21.5 - - + +
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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