Contacts of the helix formed by residues 209 - 214 (chain g) in PDB entry 5GJQ
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 TRP 209 (chain g).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177g TYR* 4.9 13.9 - + - -
178g TYR* 4.9 2.5 - + - -
207g THR* 2.9 37.1 + - - -
208g ASN* 1.3 83.4 + - - +
210g ASP* 1.3 66.5 + - - +
211g ILE* 3.3 5.6 - - + -
212g ALA* 3.1 25.1 - - + +
213g HIS* 4.5 1.6 + - - -
19o ARG* 6.2 0.2 - - - -
29o ARG* 3.8 40.6 - - + +
30o VAL* 5.0 4.0 - - + -
172o GLY* 3.4 42.4 - - - -
173o VAL* 3.8 19.5 - - + -
190o LEU* 4.1 34.2 - - + +
191o GLY* 4.3 20.1 - - - +
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Residues in contact with ASP 210 (chain g).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208g ASN* 3.0 35.3 + - - +
209g TRP* 1.3 75.2 + - - +
211g ILE* 1.3 59.4 + - + +
212g ALA 2.9 10.4 + - - -
213g HIS* 2.9 23.8 + - - +
214g MET* 4.1 8.0 - - + +
144p PRO* 4.7 23.8 - - + +
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Residues in contact with ILE 211 (chain g).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179g ARG* 5.5 1.1 - - - +
208g ASN* 6.0 2.5 - - - +
209g TRP* 5.0 2.9 - - + -
210g ASP* 1.3 79.5 - - + +
212g ALA* 1.3 61.8 + - - +
213g HIS 3.1 0.9 - - - -
214g MET* 3.3 35.3 + - + +
215g ILE* 4.7 1.0 + - - +
29o ARG* 3.6 26.5 - - + +
30o VAL* 4.1 24.0 - - + +
122p LEU* 6.3 0.7 - - + -
123p PRO* 4.1 19.3 - - + +
124p TYR* 3.2 31.2 - - + +
142p PHE* 3.9 28.3 - - + -
144p PRO* 5.8 2.0 - - + -
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Residues in contact with ALA 212 (chain g).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209g TRP* 3.1 26.1 + - + +
210g ASP 2.9 0.6 - - - -
211g ILE* 1.3 82.9 - - + +
213g HIS* 1.3 61.2 + - - +
214g MET 3.4 0.9 - - - -
215g ILE* 3.6 9.5 - - - +
30o VAL* 3.4 25.1 - - + -
173o VAL* 4.9 5.2 - - + -
175o ARG* 3.2 26.9 + - - +
188o VAL* 4.7 15.9 - - + -
190o LEU* 4.9 1.6 - - + -
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Residues in contact with HIS 213 (chain g).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209g TRP 4.7 1.2 + - - -
210g ASP* 2.9 13.9 + - - +
212g ALA* 1.3 79.6 - - - +
214g MET* 1.3 64.4 + - - +
215g ILE* 3.5 3.4 - - + +
175o ARG* 5.4 0.2 - - - -
188o VAL* 3.3 36.2 - - + +
190o LEU* 3.8 29.0 - - + +
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Residues in contact with MET 214 (chain g).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210g ASP* 4.1 7.4 - - + +
211g ILE* 3.3 44.6 + - + +
213g HIS* 1.3 83.7 - - - +
215g ILE* 1.3 65.2 + - - +
216g SER 3.8 5.7 - - - +
7p VAL* 6.6 0.2 - - - -
121p LYS 4.9 5.4 - - - +
122p LEU* 5.5 0.2 - - - -
123p PRO* 4.7 26.1 - - + +
142p PHE* 5.2 1.8 - - + -
144p PRO* 3.1 42.4 - - + -
145p ASP* 5.7 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