Contacts of the helix formed by residues 210 - 217 (chain C) in PDB entry 4GQS
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 THR 210 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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206C ARG 3.2 15.2 + - - +
207C ILE* 2.9 31.2 - - + +
208C VAL 4.0 0.9 - - - +
209C SER* 1.3 77.6 - - - +
211C PRO* 1.3 73.4 - - - +
212C TRP* 3.2 13.0 + - + +
213C ILE* 3.9 15.8 - - + +
214C GLN* 3.0 21.1 + - - +
229C THR* 5.5 4.5 - - + +
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Residues in contact with PRO 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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47C ILE* 4.1 21.9 - - + +
209C SER 3.6 3.3 - - - +
210C THR* 1.3 89.8 - - - +
212C TRP* 1.3 63.3 + - + +
214C GLN* 3.2 19.7 + - - +
215C ILE* 3.2 24.6 + - - +
474C ASN* 4.6 23.1 - - + +
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Residues in contact with TRP 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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210C THR* 3.2 11.8 + - + +
211C PRO* 1.3 81.6 - - + +
213C ILE* 1.3 95.8 + - + +
215C ILE* 2.9 30.6 - - + +
216C CYS* 3.3 23.8 + - - +
222C ILE* 3.7 37.2 - - + -
223C ILE* 4.6 0.8 - - - +
226C PHE* 3.4 57.2 + + + -
229C THR* 4.1 11.7 + - + +
230C HIS 5.8 0.2 - - - +
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Residues in contact with ILE 213 (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 LEU* 3.2 27.6 - - + -
207C ILE* 3.0 33.9 - - + +
208C VAL* 4.1 10.1 - - + +
210C THR* 3.4 5.9 + - + +
212C TRP* 1.3 97.6 - - + +
214C GLN* 1.3 65.1 + - - +
216C CYS* 3.3 14.8 + - + +
217C ASN* 3.7 10.2 + - - +
223C ILE* 4.2 13.5 - - + -
229C THR* 3.6 20.0 - - - +
230C HIS* 3.9 26.2 - - + +
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Residues in contact with GLN 214 (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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47C ILE* 5.2 5.7 - - + +
208C VAL 3.6 10.5 - - - +
209C SER* 3.1 13.7 + - - +
210C THR 3.0 21.1 + - - +
211C PRO* 3.2 17.9 - - - +
212C TRP 3.1 0.6 - - - -
213C ILE* 1.3 80.3 - - - +
215C ILE* 1.3 59.3 + - - +
216C CYS 3.6 0.3 + - - -
217C ASN* 3.7 15.9 + - - +
218C ASN* 4.3 6.4 + - - +
474C ASN 2.6 31.1 + - - +
475C GLY* 3.3 9.9 - - - -
476C PHE* 2.7 34.9 - - + +
477C ALA 4.5 0.4 - - - +
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Residues in contact with ILE 215 (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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42C ILE* 4.6 13.5 - - + -
47C ILE* 4.6 17.7 - - + -
211C PRO 3.2 10.3 + - - +
212C TRP* 2.9 35.0 - - + +
214C GLN* 1.3 77.1 - - - +
216C CYS* 1.3 65.5 + - - +
217C ASN 3.3 1.1 - - - -
218C ASN* 3.2 27.0 + - - +
219C PHE* 3.4 32.1 - - + -
222C ILE* 5.9 7.2 - - + -
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Residues in contact with CYS 216 (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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101C PRO* 5.1 0.3 - - - +
212C TRP* 3.3 35.8 + - - +
213C ILE* 3.5 13.2 - - - +
214C GLN 3.3 0.4 - - - -
215C ILE* 1.3 76.1 - - - +
217C ASN* 1.3 66.6 + - - +
218C ASN 3.0 1.8 - - - -
219C PHE 2.7 26.6 - - - +
220C PRO* 3.4 4.9 - - - +
222C ILE* 3.5 25.6 - - - -
223C ILE* 3.5 42.0 - - + +
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Residues in contact with ASN 217 (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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99C HIS* 4.3 5.8 + - - -
100C PHE* 3.5 33.8 - - - +
101C PRO* 2.9 57.7 - - + +
102C LEU* 3.0 36.1 + - - +
213C ILE 3.7 5.3 + - - +
214C GLN* 3.9 12.1 - - - +
215C ILE 3.3 0.6 - - - -
216C CYS* 1.3 77.6 - - - +
218C ASN* 1.3 65.9 + - - +
220C PRO* 4.1 3.3 - - - +
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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