Contacts of the helix formed by residues 169 - 177 (chain C) in PDB entry 4RQE
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 169 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168C TYR* 1.3 77.7 - - - +
170C HIS* 1.3 64.2 + - - +
171C VAL* 3.0 29.5 + - - +
172C ASP* 3.3 19.7 + - - +
173C LEU* 3.3 19.6 + - - +
385C GLY 4.0 6.0 + - - -
386C SER* 4.1 10.9 + - - -
442C GLU* 3.6 6.7 - - - -
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Residues in contact with HIS 170 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169C SER* 1.3 76.8 + - - +
171C VAL* 1.3 66.9 + - + +
173C LEU* 4.2 11.4 - - - -
174C VAL* 3.7 22.2 + - - +
311C ASP* 5.7 3.4 + - + -
314C GLY* 3.8 26.8 - - - -
315C ILE* 3.9 9.2 + - - +
316C PHE* 4.1 17.2 - - + +
383C PHE* 3.7 23.0 - + - -
386C SER* 3.8 13.5 - - - -
390C ARG* 4.6 12.2 + - - -
438C CYS* 3.5 38.2 - - + +
441C LEU* 4.6 6.1 - - + +
442C GLU* 3.1 17.4 + - + +
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Residues in contact with VAL 171 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169C SER* 3.0 15.4 - - - +
170C HIS* 1.3 87.3 - - + +
172C ASP* 1.3 71.9 + - - +
174C VAL* 3.3 19.7 - - + +
175C VAL* 3.4 12.5 - - + +
180C PHE* 6.2 0.9 - - + -
313C ARG* 3.6 35.2 - - + +
314C GLY* 3.7 26.0 - - - +
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Residues in contact with ASP 172 (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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168C TYR* 5.4 2.8 - - - -
169C SER* 3.3 24.0 + - - +
171C VAL* 1.3 85.6 - - - +
173C LEU* 1.3 66.0 + - + +
175C VAL* 2.9 10.1 + - - +
176C MET* 2.9 36.0 + - + +
474C ALA* 4.8 21.8 - - + +
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Residues in contact with LEU 173 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168C TYR* 3.3 35.4 - - + +
169C SER 3.3 12.0 + - - +
170C HIS* 4.3 6.1 - - - -
171C VAL 3.5 0.2 - - - -
172C ASP* 1.3 79.0 - - + +
174C VAL* 1.3 56.7 + - - +
176C MET* 3.3 25.6 + - + +
177C VAL* 3.0 35.9 + - - +
441C LEU* 3.3 43.5 - - + +
442C GLU* 4.1 5.8 - - + -
445C GLN* 3.8 11.9 - - + +
450C ILE* 4.4 5.2 - - + -
470C PHE* 3.7 19.3 - - + -
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Residues in contact with VAL 174 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170C HIS 3.7 14.8 + - - +
171C VAL* 3.3 17.5 - - + +
173C LEU* 1.3 77.7 - - - +
175C VAL* 1.3 60.0 + - - +
177C VAL* 4.1 5.9 - - + +
178C ASP 3.6 0.2 + - - -
179C GLY* 3.3 31.0 + - - +
180C PHE* 3.6 43.6 - - + +
196C LEU* 5.6 1.8 - - + -
200C LEU* 5.5 7.2 - - + -
313C ARG 6.1 0.4 - - - +
314C GLY* 6.3 1.1 - - - -
315C ILE* 4.4 24.0 - - + -
441C LEU* 4.4 15.7 - - + +
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Residues in contact with VAL 175 (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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171C VAL* 3.4 19.7 - - + +
172C ASP* 2.9 9.1 + - - +
174C VAL* 1.3 82.7 - - + +
176C MET* 1.3 60.6 + - - +
177C VAL 3.2 1.3 - - - -
178C ASP* 2.8 17.2 + - - +
180C PHE* 4.4 20.2 - - + +
472C LYS* 3.2 40.8 - - + +
473C PRO 4.5 8.5 - - - +
474C ALA 5.4 5.2 - - - -
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Residues in contact with MET 176 (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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168C TYR* 5.3 4.9 - - + -
172C ASP* 2.9 21.1 + - + +
173C LEU* 3.6 39.3 - - + +
175C VAL* 1.3 75.9 - - - +
177C VAL* 1.3 59.2 + - - +
470C PHE* 3.5 28.8 - - + -
471C VAL 3.1 24.6 + - - -
472C LYS* 3.1 21.3 + - - +
473C PRO* 3.2 19.1 - - - +
474C ALA* 3.6 26.9 - - + -
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Residues in contact with VAL 177 (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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173C LEU 3.0 22.3 + - - +
174C VAL* 4.4 6.3 - - + +
176C MET* 1.3 76.9 - - - +
178C ASP* 1.3 68.4 + - - +
179C GLY* 4.3 9.0 - - - +
199C VAL* 4.5 13.2 - - + +
200C LEU* 5.3 5.4 - - + +
441C LEU* 4.8 7.4 - - + -
450C ILE* 4.1 13.9 - - + -
468C ILE* 3.6 30.3 - - + -
469C PRO 4.2 6.7 - - - +
470C PHE* 3.7 20.9 - - + -
471C VAL* 3.7 10.4 - - - +
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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