Contacts of the helix formed by residues 204 - 211 (chain C) in PDB entry 1EQB
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 VAL 204 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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174C PHE* 3.9 30.7 - - + -
183C TRP* 5.1 4.5 - - + -
201C MET* 3.0 24.9 + - + +
203C HIS* 1.3 79.5 - - + +
205C ALA* 1.3 59.5 + - - +
206C GLY 3.2 2.9 - - - -
207C LEU* 3.1 10.1 + - + +
208C VAL* 2.8 32.5 + - + +
213C TYR* 4.0 43.1 - - + -
230C THR* 3.6 1.1 - - - -
316C ASN* 4.4 3.6 - - + -
317C HIS* 4.2 12.6 - - + +
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Residues in contact with ALA 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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86C PHE* 3.6 12.7 - - + -
201C MET* 2.8 19.0 + - - +
202C ALA 3.9 5.4 - - - +
203C HIS 3.6 0.6 - - - -
204C VAL* 1.3 77.2 - - - +
206C GLY* 1.3 57.4 + - - +
208C VAL* 3.4 0.4 + - - -
209C ALA* 2.9 29.3 + - - +
225C THR* 2.9 31.9 - - - +
226C THR 4.5 1.6 - - - +
230C THR* 3.5 1.2 + - - -
231C LEU* 4.1 21.5 - - + -
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Residues in contact with GLY 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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205C ALA* 1.3 74.2 - - - +
207C LEU* 1.3 60.7 + - - -
209C ALA* 3.1 5.4 + - - +
210C ALA 3.1 17.3 + - - -
230C THR* 2.7 42.5 + - - -
231C LEU* 3.7 13.2 - - - +
284C PHE* 3.8 1.3 - - - -
288C GLN* 3.5 15.5 - - - +
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Residues in contact with LEU 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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204C VAL* 3.1 14.7 + - + +
206C GLY* 1.3 75.8 - - - +
208C VAL* 1.3 59.1 + - - +
210C ALA* 3.3 1.7 + - - -
211C GLY 3.0 3.5 + - - -
212C VAL* 2.7 46.4 + - + +
213C TYR* 3.7 20.6 - - + -
230C THR* 3.9 9.2 + - + -
288C GLN* 3.1 45.3 - - + +
291C VAL* 4.6 11.0 - - + -
292C ALA* 5.2 2.7 - - + +
315C ASP 5.1 0.4 - - - +
316C ASN* 3.8 33.4 - - + -
317C HIS* 3.8 14.1 - - - +
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Residues in contact with VAL 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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86C PHE* 4.2 13.0 - - + -
201C MET* 4.1 13.2 - - - -
204C VAL* 2.8 34.4 + - + +
205C ALA 3.7 4.9 - - - +
207C LEU* 1.3 72.5 - - - +
209C ALA* 1.3 63.4 + - - +
211C GLY* 2.8 20.6 + - - -
213C TYR* 3.7 14.3 - - + +
214C PRO 3.7 17.7 - - - +
215C ASN* 3.5 44.9 + - + +
216C PRO* 4.2 2.2 - - + -
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Residues in contact with ALA 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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85C LEU* 4.1 44.2 - - + +
86C PHE* 4.1 9.2 - - + -
205C ALA 2.9 15.7 + - - +
206C GLY* 3.1 11.9 + - - +
208C VAL* 1.3 78.7 - - - +
210C ALA* 1.3 59.3 + - - +
211C GLY 3.4 0.3 + - - -
231C LEU* 4.3 2.5 - - + -
279C ALA 5.1 0.9 - - - +
284C PHE* 3.9 17.0 - - + -
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Residues in contact with ALA 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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206C GLY 3.1 4.9 + - - -
207C LEU 3.8 3.8 - - - +
209C ALA* 1.3 76.7 - - - +
211C GLY* 1.3 60.0 + - - +
212C VAL* 3.7 5.5 + - + +
284C PHE* 4.2 4.7 - - + +
285C LYS* 3.1 57.8 - - + +
288C GLN* 3.4 37.7 - - + -
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Residues in contact with GLY 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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208C VAL 2.8 16.7 + - - -
209C ALA 3.2 0.8 + - - -
210C ALA* 1.3 80.0 - - - +
212C VAL* 1.3 62.4 + - - +
213C TYR 3.4 7.9 + - - -
285C LYS* 5.3 0.9 - - - -
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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