Contacts of the helix formed by residues 198 - 212 (chain C) in PDB entry 2AYN
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 198 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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197C GLN* 1.3 80.2 + - - +
199C ALA* 1.3 54.5 + - - +
200C ASN* 2.5 37.8 + - - +
201C GLU* 2.6 53.8 + - + +
202C CYS* 3.0 9.2 + - - +
330C PHE* 5.3 0.5 - - - -
430C SER* 3.3 22.2 + - - +
435C TYR* 3.5 5.2 - - - -
475C TYR* 3.0 20.9 + - - -
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Residues in contact with ALA 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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114C TYR* 3.6 25.1 - - + +
118C THR* 3.1 11.0 + - - +
197C GLN 3.3 6.5 + - - -
198C ASP* 1.3 71.8 + - - +
200C ASN* 1.3 49.9 + - - +
202C CYS* 3.2 2.8 + - - -
203C TRP* 2.6 32.2 + - - +
423C LEU* 3.9 16.4 - - + -
435C TYR* 3.0 41.5 - - + -
475C TYR* 4.8 0.9 - - + -
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Residues in contact with ASN 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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198C ASP* 2.5 21.4 + - - +
199C ALA* 1.3 70.6 - - - +
201C GLU* 1.3 56.2 + - - +
203C TRP* 2.7 31.8 + - - +
204C ILE* 2.9 20.5 + - - +
273C GLN* 2.9 32.0 + - - +
326C GLN* 3.3 28.9 + - - +
475C TYR* 3.1 23.0 - - + +
476C VAL* 3.4 23.8 - - - +
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Residues in contact with GLU 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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184C GLN* 4.8 9.5 - - - +
185C PHE* 4.2 17.2 - - + -
197C GLN* 5.8 0.4 - - - +
198C ASP* 2.6 38.9 + - + +
200C ASN* 1.3 71.8 + - - +
202C CYS* 1.3 62.8 + - - +
204C ILE* 3.3 17.6 + - - +
205C GLN* 3.0 47.6 + - - +
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Residues in contact with CYS 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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114C TYR* 3.7 35.0 - - + -
115C MET* 4.2 6.7 - - - -
118C THR* 3.6 24.0 - - - +
178C LEU* 4.3 11.9 - - - -
185C PHE* 3.7 14.0 - - + -
198C ASP 3.0 2.6 + - - +
199C ALA 3.4 8.3 - - - +
201C GLU* 1.3 76.3 - - - +
203C TRP* 1.3 72.9 + - - +
205C GLN* 4.5 0.2 - - - -
206C MET* 3.0 41.4 + - - +
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Residues in contact with TRP 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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118C THR* 3.9 16.6 - - + +
121C CYS* 3.5 36.8 - - + -
122C ILE* 4.6 11.6 - - + +
199C ALA 2.6 17.6 + - - +
200C ASN* 2.7 22.4 + - - +
202C CYS* 1.3 80.6 - - - +
204C ILE* 1.3 65.0 + - - +
206C MET* 3.0 9.4 + - - +
207C MET* 3.0 53.7 + - + +
246C PHE* 5.9 1.3 - + - -
273C GLN* 4.3 13.9 - - + -
324C THR* 3.6 23.2 - - + +
423C LEU* 4.3 14.4 - - + -
476C VAL* 3.5 32.8 - - + -
478C LEU* 4.5 20.4 - - + -
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Residues in contact with ILE 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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200C ASN* 2.9 30.2 + - - +
201C GLU* 3.8 18.4 - - - +
203C TRP* 1.3 77.6 - - - +
205C GLN* 1.3 59.3 + - + +
207C MET* 2.9 7.7 + - + +
208C ARG* 2.7 53.8 + - + +
272C LEU* 6.5 0.9 - - + -
273C GLN* 4.1 22.0 - - + +
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Residues in contact with GLN 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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182C PHE* 3.0 47.7 - - + -
184C GLN* 4.9 4.1 - - - +
185C PHE* 4.5 6.3 - - + -
201C GLU* 3.0 37.6 + - - +
202C CYS* 4.0 5.4 - - - +
204C ILE* 1.3 82.8 - - + +
206C MET* 1.3 58.5 + - + +
208C ARG* 3.8 27.7 + - - +
209C VAL* 2.8 28.3 + - - +
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Residues in contact with MET 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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115C MET* 5.3 2.5 - - - -
118C THR* 4.0 1.8 - - + -
119C VAL* 4.9 8.3 - - - -
122C ILE* 3.7 26.0 - - + -
151C ILE* 4.2 21.8 - - + -
155C LEU* 4.1 35.4 - - + -
174C LEU* 4.8 6.3 - - + -
178C LEU* 4.3 18.2 - - + -
202C CYS* 3.0 38.3 + - - +
203C TRP 3.0 3.9 + - - +
205C GLN* 1.3 75.0 - - + +
207C MET* 1.3 68.3 + - - +
209C VAL* 3.0 17.9 + - - +
210C LEU* 3.0 20.2 + - + +
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Residues in contact with MET 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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122C ILE* 5.0 14.4 - - + -
128C LEU* 5.4 1.8 - - + -
203C TRP* 3.0 55.5 + - + +
204C ILE* 2.9 10.2 + - + +
206C MET* 1.3 78.3 - - + +
208C ARG* 1.3 52.0 + - - +
209C VAL 3.1 0.3 + - - -
210C LEU* 3.2 13.8 + - - +
211C GLN* 2.6 37.8 + - - +
242C ILE* 4.0 20.5 - - + +
246C PHE* 3.6 46.2 - - + -
272C LEU* 5.2 11.0 - - + +
324C THR* 4.6 4.0 - - - +
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Residues in contact with ARG 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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204C ILE* 2.7 36.7 + - + +
205C GLN* 3.8 29.7 + - - +
207C MET* 1.3 71.7 - - - +
209C VAL* 1.3 68.0 + - + +
211C GLN* 3.0 31.9 + - - +
212C GLN* 3.1 28.7 + - - +
272C LEU* 5.6 2.6 - - - +
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Residues in contact with VAL 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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148C ALA* 3.3 46.9 - - + +
151C ILE* 4.4 16.2 - - + -
152C THR* 3.6 10.8 - - - +
182C PHE* 4.1 18.6 - - + -
205C GLN* 2.8 21.8 - - - +
206C MET* 3.0 9.8 + - - +
208C ARG* 1.3 75.6 - - + +
210C LEU* 1.3 69.1 + - + +
212C GLN* 2.6 32.5 + - - +
213C LYS* 3.4 1.7 + - + +
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Residues in contact with LEU 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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122C ILE* 4.2 18.4 - - + -
128C LEU* 4.7 4.7 - - + -
132C LEU* 4.1 20.6 - - + -
151C ILE* 6.6 0.2 - - + -
152C THR* 4.2 12.6 - - + -
155C LEU* 4.2 24.0 - - + -
206C MET* 3.0 21.2 + - + +
207C MET* 3.4 11.9 - - - +
209C VAL* 1.3 79.2 - - + +
211C GLN* 1.3 61.8 + - - +
213C LYS* 2.9 4.1 + - - +
214C LEU* 2.7 65.7 + - + +
242C ILE* 3.8 14.4 - - + -
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Residues in contact with GLN 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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207C MET 2.6 18.2 + - - +
208C ARG* 3.0 35.3 + - - +
209C VAL 2.7 2.2 + - - -
210C LEU* 1.3 72.3 - - - +
212C GLN* 1.3 57.8 + - + +
213C LYS 3.4 2.8 + - - -
214C LEU 4.3 1.9 - - - +
240C SER* 2.5 34.2 + - - +
242C ILE* 3.3 24.1 - - + +
243C ASP* 3.9 27.5 + - - +
272C LEU* 3.7 23.6 - - + +
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Residues in contact with GLN 212 (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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148C ALA* 5.0 11.1 - - + +
208C ARG* 3.2 32.3 + - - +
209C VAL* 2.6 25.6 + - - +
211C GLN* 1.3 78.7 + - + +
213C LYS* 1.3 78.5 + - + +
240C SER* 4.4 3.1 - - - -
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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