Contacts of the helix formed by residues 199 - 207 (chain C) in PDB entry 3E9B
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 199 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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308B ARG 4.4 0.2 - - - -
309B GLU* 3.9 25.1 + - - +
178C GLY 4.5 0.2 - - - -
179C LEU* 3.2 33.2 - - - +
197C TYR* 3.9 5.6 - - - -
198C PHE* 1.3 80.0 - - - +
200C MET* 1.3 65.4 + - - +
201C THR* 3.2 18.6 + - - -
202C GLU* 2.7 28.0 + - - -
203C VAL* 3.0 17.0 + - - +
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Residues in contact with MET 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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255B ARG* 3.2 51.6 - - - +
308B ARG* 3.5 24.2 - - - +
178C GLY* 3.4 37.0 - - - +
179C LEU 2.9 14.5 + - - +
180C ARG* 3.9 9.2 - - + +
199C SER* 1.3 73.2 - - - +
201C THR* 1.3 57.2 + - - +
203C VAL* 3.6 4.8 - - + +
204C ASP* 2.9 36.4 + - - +
250C GLY 3.5 11.7 - - - +
251C GLY* 3.7 1.1 - - - -
252C LEU* 3.7 33.2 - - + +
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Residues in contact with THR 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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259B TYR* 3.6 16.0 - - + -
262B GLU* 2.8 40.8 + - + +
263B GLU* 5.6 2.5 - - - +
266B LYS* 5.6 6.3 - - + +
307B LYS* 5.6 0.7 - - - +
308B ARG* 3.4 18.6 + - - +
309B GLU* 4.8 2.2 + - - -
199C SER* 3.0 12.4 + - - -
200C MET* 1.3 80.1 - - - +
202C GLU* 1.3 73.4 + - - +
204C ASP* 3.4 3.2 + - - +
205C LYS* 3.2 23.0 + - - +
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Residues in contact with GLU 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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309B GLU* 4.9 6.5 - - - +
197C TYR* 3.9 18.2 - - - +
198C PHE* 3.9 28.9 - - + -
199C SER* 2.7 39.1 + - - +
201C THR* 1.3 88.7 - - - +
203C VAL* 1.3 59.8 + - - +
205C LYS* 4.6 12.6 + - - +
206C LEU* 3.0 41.8 + - + +
211C VAL* 4.0 1.5 - - - +
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Residues in contact with VAL 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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255B ARG* 3.5 21.1 + - - +
177C ILE* 4.7 8.5 - - + -
198C PHE 4.0 10.5 - - - +
199C SER 3.0 21.0 + - - +
200C MET* 3.6 12.8 - - + +
202C GLU* 1.3 76.0 - - - +
204C ASP* 1.3 57.2 + - - +
207C GLY* 2.8 27.9 + - - -
208C ILE* 4.4 13.2 - - + +
211C VAL* 3.9 17.9 - - + -
252C LEU* 4.1 21.5 - - + -
256C GLU* 3.6 17.7 - - - +
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Residues in contact with ASP 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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207B GLY* 5.5 1.4 - - - -
208B ILE* 3.8 20.6 + - + +
209B GLY 4.3 1.9 + - - -
255B ARG* 2.8 52.1 + - - +
256B GLU* 5.0 1.8 - - - -
259B TYR* 4.0 14.1 - - + -
308B ARG* 2.7 35.3 + - - -
200C MET 2.9 17.1 + - - +
201C THR 3.6 4.9 - - - +
203C VAL* 1.3 78.5 - - - +
205C LYS* 1.3 62.0 + - - +
207C GLY* 4.5 2.3 + - - -
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Residues in contact with LYS 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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207B GLY* 6.1 0.7 - - - -
209B GLY* 4.1 22.5 + - - +
210B LYS 5.3 0.2 + - - -
213B GLU* 5.4 9.3 + - - +
259B TYR* 3.0 38.1 + - + +
263B GLU* 5.5 2.6 + - - -
266B LYS* 5.5 4.9 - - - +
201C THR* 3.2 8.5 + - - +
202C GLU* 4.0 11.7 + - - +
203C VAL 3.3 0.2 - - - -
204C ASP* 1.3 82.1 - - - +
206C LEU* 1.3 94.7 + - + +
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Residues in contact with LEU 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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198C PHE* 4.1 18.4 - - + -
202C GLU* 3.0 21.2 + - + +
205C LYS* 1.3 105.3 - - + +
207C GLY* 1.3 67.1 + - - +
210C LYS* 3.8 24.8 + - + +
211C VAL* 4.3 4.3 - - + -
214C GLU* 3.5 32.8 - - - +
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Residues in contact with GLY 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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204A ASP 5.9 1.1 - - - -
203C VAL 2.8 19.3 + - - -
204C ASP 5.0 2.0 - - - -
205C LYS 3.5 1.0 - - - -
206C LEU* 1.3 77.8 - - - +
208C ILE* 1.3 67.4 + - - -
209C GLY 3.0 4.9 + - - -
210C LYS 3.1 4.4 + - - -
211C VAL* 3.0 20.6 + - - +
256C GLU* 5.9 0.2 - - - -
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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