Contacts of the helix formed by residues 164 - 176 (chain A) in PDB entry 3RKQ
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 164 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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163A LEU* 1.3 75.7 - - - +
165A ALA* 1.3 59.8 + - - +
166A PRO* 3.1 17.2 - - - +
167A GLU* 2.6 35.4 + - - +
168A ARG* 2.8 29.8 + - - +
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Residues in contact with ALA 165 (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 SER* 1.3 72.3 - - - +
166A PRO* 1.3 66.4 - - + +
168A ARG* 3.7 23.9 - - - +
169A ASP* 2.8 43.0 + - - +
179A SER* 5.9 0.2 - - - -
11D C 4.8 4.3 - - - +
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Residues in contact with PRO 166 (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 SER* 3.1 16.8 - - - +
165A ALA* 1.3 96.9 - - + +
167A GLU* 1.3 55.4 + - + +
169A ASP* 4.0 6.8 - - + +
170A GLN* 3.1 29.5 + - - +
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Residues in contact with GLU 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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156A ARG* 4.4 11.4 + - - +
160A GLN* 3.1 30.8 + - - +
162A TYR 4.2 0.3 - - - +
163A LEU* 3.2 23.5 - - + +
164A SER* 2.6 43.6 + - - +
166A PRO* 1.3 79.2 - - + +
168A ARG* 1.3 62.2 + - - +
170A GLN* 3.6 5.1 + - - +
171A LEU* 3.2 24.9 + - - +
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Residues in contact with ARG 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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163A LEU* 2.6 57.3 + - + +
164A SER* 2.8 20.0 + - - +
165A ALA* 3.7 21.5 - - - +
167A GLU* 1.3 76.8 - - - +
169A ASP* 1.3 59.3 + - - +
171A LEU* 3.6 1.7 + - - +
172A ALA* 3.1 28.2 + - - +
179A SER* 3.8 13.8 + - - +
182A VAL* 4.0 10.8 - - + +
183A LYS* 3.8 39.0 - - - +
186A PHE* 5.9 3.1 - - - -
11D C 2.6 62.3 + - - -
12D C 4.3 4.6 + - - -
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Residues in contact with ASP 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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165A ALA* 2.8 29.8 + - - +
166A PRO* 4.0 6.2 - - + +
168A ARG* 1.3 73.9 - - - +
170A GLN* 1.3 61.3 + - - +
172A ALA* 3.7 4.4 - - - +
173A SER* 3.0 29.5 + - - -
179A SER* 2.5 35.1 + - - -
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Residues in contact with GLN 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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166A PRO 3.1 19.7 + - - +
167A GLU* 4.0 5.8 - - - +
169A ASP* 1.3 77.1 - - - +
171A LEU* 1.3 58.9 + - - +
173A SER* 2.7 24.2 + - - +
174A VAL* 3.1 24.0 - - + +
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Residues in contact with LEU 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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152A GLU* 4.1 11.2 - - + +
153A LEU* 4.1 8.7 - - + -
156A ARG* 3.9 38.1 - - + +
163A LEU* 3.9 22.4 - - + -
167A GLU 3.2 17.3 + - - +
168A ARG 4.0 4.0 - - - +
170A GLN* 1.3 75.6 - - - +
172A ALA* 1.3 65.3 + - - +
174A VAL* 3.3 7.9 + - + +
175A LEU* 3.0 53.9 + - + +
182A VAL* 4.2 7.0 - - + -
186A PHE* 3.9 18.4 - - + -
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Residues in contact with ALA 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 ARG 3.1 19.7 + - - +
169A ASP* 3.7 6.5 - - - +
171A LEU* 1.3 77.2 - - - +
173A SER* 1.3 64.6 + - - +
175A LEU 3.2 1.4 + - - +
176A LYS* 3.0 19.9 + - - -
177A LEU* 3.1 29.4 + - - +
178A THR 3.6 20.2 - - - +
179A SER* 3.7 5.4 - - - +
182A VAL* 3.7 11.9 - - + +
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Residues in contact with SER 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 ASP 3.0 15.3 + - - -
170A GLN* 2.7 18.3 + - - +
172A ALA* 1.3 76.0 - - - +
174A VAL* 1.3 71.0 + - - +
176A LYS* 2.9 34.3 + - - +
177A LEU 4.9 0.4 - - - -
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Residues in contact with VAL 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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152A GLU* 5.1 7.0 - - + +
170A GLN* 3.1 24.0 + - + +
171A LEU* 3.5 14.8 - - + +
172A ALA 3.2 0.2 - - - -
173A SER* 1.3 85.4 + - - +
175A LEU* 1.3 73.0 + - + +
176A LYS* 3.7 11.3 + - - +
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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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148A ALA 5.1 0.4 - - - +
149A GLN* 2.7 53.9 + - + +
152A GLU* 3.5 32.3 - - + -
153A LEU* 3.7 36.8 - - + -
171A LEU* 3.0 36.5 + - + +
172A ALA 4.1 1.8 - - - +
174A VAL* 1.3 82.9 - - + +
176A LYS* 1.3 62.8 + - - +
177A LEU* 4.4 14.1 - - + -
182A VAL* 5.0 1.8 - - + -
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Residues in contact with LYS 176 (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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149A GLN* 4.3 4.3 + - - +
172A ALA 3.0 5.7 + - - -
173A SER* 2.9 31.4 + - - +
174A VAL* 3.8 11.0 + - - +
175A LEU* 1.3 81.6 - - - +
177A LEU* 1.3 64.3 + - - +
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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