Contacts of the helix formed by residues 166 - 175 (chain A) in PDB entry 3QD4
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 GLU 166 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88A LEU 5.3 4.7 - - - +
164A ASN 3.8 0.6 + - - -
165A GLY* 1.3 73.9 - - - -
167A LEU* 1.3 65.0 + - - +
168A LEU* 3.8 24.8 - - - +
169A LYS* 3.2 27.1 + - + +
170A TYR* 3.5 9.7 - - - -
208A PRO 3.9 3.8 - - - +
209A GLU* 3.2 37.5 - - - +
212A LEU* 3.9 12.3 - - + -
213A LEU* 4.3 0.9 - - - -
360A 3Q6 6.2 1.8 - - + -
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Residues in contact with LEU 167 (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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165A GLY 3.8 0.6 + - - -
166A GLU* 1.3 71.9 - - - +
168A LEU* 1.3 62.3 + - - +
170A TYR* 3.2 4.4 + - + -
171A ILE* 3.1 25.7 + - + +
177A PHE* 4.2 28.0 - - + -
185A TYR* 5.1 10.3 - - + -
189A ILE* 4.6 6.5 - - + -
208A PRO* 3.4 12.5 + - + +
211A ILE* 2.9 54.0 + - + +
213A LEU* 3.8 27.0 - - + +
219A ILE* 5.6 1.3 - - + -
271A ILE* 4.5 9.2 - - + -
275A LEU* 4.3 15.5 - - + -
358A LEU* 6.2 0.4 - - + -
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Residues in contact with LEU 168 (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 GLU* 3.1 17.4 - - - +
167A LEU* 1.3 76.8 - - - +
169A LYS* 1.3 62.8 + - - +
171A ILE* 3.3 8.9 + - + +
172A ARG* 3.0 66.6 + - + +
208A PRO* 3.2 28.1 + - + +
209A GLU* 3.7 28.5 - - + +
248A TYR* 5.6 0.2 - - - +
274A GLN* 4.1 23.1 - - - +
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Residues in contact with LYS 169 (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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163A LYS 5.3 0.4 + - - -
164A ASN* 3.0 33.7 + - - +
165A GLY* 4.6 2.0 - - - -
166A GLU* 3.2 18.3 + - + +
168A LEU* 1.3 79.3 - - - +
170A TYR* 1.3 77.8 + - - +
172A ARG* 3.2 10.3 + - - +
173A LYS* 2.8 43.2 + - + +
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Residues in contact with TYR 170 (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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164A ASN* 3.2 50.2 + - + +
166A GLU 3.5 5.8 - - - -
167A LEU* 3.2 6.1 + - - +
169A LYS* 1.3 89.9 + - - +
171A ILE* 1.3 64.6 + - - +
173A LYS* 3.6 29.1 + - + +
174A ILE* 3.0 30.2 + - + +
177A PHE* 4.2 8.5 - - + -
213A LEU* 3.4 26.5 - - + -
217A MET* 3.7 17.9 - - + -
358A LEU* 3.7 32.5 - - + -
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Residues in contact with ILE 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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167A LEU* 3.1 17.4 + - + +
168A LEU* 3.6 11.2 - - + +
170A TYR* 1.3 75.2 - - - +
172A ARG* 1.3 58.9 + - + +
175A GLY* 2.9 39.4 + - - +
176A SER* 5.4 0.9 - - - -
177A PHE* 4.1 12.3 - - + -
208A PRO* 4.2 23.8 - - + -
271A ILE* 5.6 0.4 - - + +
274A GLN* 4.1 36.6 - - + +
275A LEU* 3.9 31.4 - - + -
278A GLY 4.0 20.6 - - - +
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Residues in contact with ARG 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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168A LEU* 3.0 56.2 + - + +
169A LYS* 3.6 9.0 - - - +
171A ILE* 1.3 78.5 - - + +
173A LYS* 1.3 62.4 + - - +
175A GLY* 3.9 4.9 + - - -
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Residues in contact with LYS 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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169A LYS* 2.8 32.7 + - + +
170A TYR* 3.6 37.8 + - + +
171A ILE 3.2 0.4 - - - -
172A ARG* 1.3 79.4 - - - +
174A ILE* 1.3 74.2 + - + +
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Residues in contact with ILE 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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170A TYR* 3.0 19.2 + - + +
171A ILE 4.6 0.2 - - - +
173A LYS* 1.3 95.8 - - + +
175A GLY* 1.3 57.8 + - - +
176A SER 3.2 16.2 + - - +
177A PHE* 3.5 36.6 - - + -
358A LEU* 3.8 45.5 - - + +
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Residues in contact with GLY 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 ILE* 2.9 22.1 + - - +
172A ARG* 3.9 4.6 + - - -
173A LYS 3.5 2.6 + - - -
174A ILE* 1.3 75.3 - - - +
176A SER* 1.3 62.7 + - - -
278A GLY* 3.2 19.8 - - - +
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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