Contacts of the helix formed by residues 170 - 175 (chain A) in PDB entry 3QTS
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 ALA 170 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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168A TYR 3.5 3.8 + - - -
169A ARG* 1.3 75.8 - - - +
171A PRO* 1.3 73.1 - - + +
172A GLU* 3.3 27.4 - - + +
173A ILE* 3.1 20.5 + - + +
174A LEU* 3.3 9.8 + - - +
184A VAL* 4.0 18.1 + - + +
187A TRP* 3.4 24.0 - - + -
188A SER* 5.0 1.0 + - - -
274A ARG* 3.9 0.9 - - - +
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Residues in contact with PRO 171 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169A ARG 3.7 0.2 - - - -
170A ALA* 1.3 86.4 - - + +
172A GLU* 1.3 64.9 + - - +
174A LEU* 3.2 14.2 + - + +
175A LEU* 2.9 34.1 + - + +
187A TRP* 3.4 38.4 - - + -
212A LEU* 4.6 11.0 - - + -
215A ILE* 4.6 4.9 - - + -
216A PHE* 5.3 0.2 - - + -
227A TRP* 3.9 17.9 - - + -
269A TYR* 4.0 22.0 - - + -
274A ARG* 3.9 8.7 - - - +
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Residues in contact with GLU 172 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170A ALA* 3.4 11.2 - - - +
171A PRO* 1.3 74.8 - - - +
173A ILE* 1.3 63.8 + - + +
175A LEU* 3.4 8.8 + - - +
176A GLY 3.5 0.2 + - - -
177A CYS* 3.0 46.4 + - + +
179A TYR 5.7 2.0 - - - +
180A TYR* 6.3 0.7 - - - -
181A SER* 4.8 0.9 + - - +
183A ALA* 4.2 0.3 - - - +
184A VAL* 3.5 24.4 + - + +
227A TRP* 3.6 23.0 - - + -
233A MET* 4.9 2.5 - - + -
269A TYR 4.2 0.5 - - - +
271A PRO* 3.5 23.7 - - + +
274A ARG* 2.8 44.2 + - - -
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Residues in contact with ILE 173 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126A ARG* 4.7 12.1 - - + +
169A ARG* 4.1 26.5 - - - +
170A ALA 3.1 19.2 + - - +
172A GLU* 1.3 79.8 - - + +
174A LEU* 1.3 57.2 + - - +
176A GLY* 3.0 20.3 + - - -
177A CYS 4.2 8.0 + - - +
180A TYR* 4.1 30.5 - - + +
184A VAL* 3.7 38.6 - - + -
208A GLU* 5.5 0.7 - - - +
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Residues in contact with LEU 174 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166A LEU* 5.2 3.4 - - + -
169A ARG* 3.9 30.7 - - + +
170A ALA 3.3 8.3 + - - +
171A PRO* 3.2 6.9 + - + +
173A ILE* 1.3 76.5 - - - +
175A LEU* 1.3 61.1 + - - +
176A GLY 3.1 3.9 + - - -
208A GLU* 4.2 42.7 - - + +
211A GLN* 3.6 30.3 - - + -
212A LEU* 3.9 28.2 - - + +
215A ILE* 3.7 23.1 - - + -
235A ASP* 3.8 10.9 - - - +
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Residues in contact with LEU 175 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171A PRO* 2.9 19.1 + - + +
172A GLU 3.4 4.5 + - - +
173A ILE 3.2 0.6 - - - -
174A LEU* 1.3 75.3 - - - +
176A GLY* 1.3 61.2 + - - +
177A CYS 3.4 2.2 - - - -
212A LEU* 3.5 33.2 - - + -
216A PHE* 4.8 7.2 - - + -
227A TRP* 3.9 25.6 - - + -
230A VAL* 3.9 18.2 - - + -
233A MET* 4.2 15.3 - - + -
234A PRO* 3.4 9.0 - - - +
235A ASP* 2.9 28.3 + - + +
236A TYR* 4.0 14.8 - - + +
240A PHE* 3.7 22.2 - - + -
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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