Contacts of the helix formed by residues 164 - 171 (chain L) in PDB entry 3CPW
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 THR 164 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4320 G 4.4 0.4 - - - -
99L ARG* 5.6 0.7 - - - -
102L GLU* 2.7 37.3 + - - +
114L VAL* 3.9 17.7 + - + +
115L LEU 5.2 1.7 + - - -
116L ASN* 5.2 5.2 - - - +
158L ARG* 4.2 15.6 + - - +
159L VAL* 4.2 16.1 - - - +
162L GLY* 3.2 2.0 - - - -
163L LEU* 1.3 82.3 - - - +
165L GLY* 1.3 67.1 + - - +
166L ALA 3.0 16.8 - - - +
167L GLY* 3.3 8.5 - - - +
168L ARG* 2.7 35.9 + - - +
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Residues in contact with GLY 165 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4320 G 2.9 31.1 + - - -
115L LEU 5.5 1.4 + - - -
116L ASN* 4.5 6.3 + - - -
164L THR* 1.3 78.6 - - - +
166L ALA* 1.3 60.0 + - - -
168L ARG* 3.4 6.2 + - - +
169L ARG* 3.1 42.2 + - - +
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Residues in contact with ALA 166 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96L ASP* 4.5 8.3 - - - +
98L GLN* 3.8 37.2 - - + +
99L ARG* 4.1 7.4 - - - +
102L GLU* 4.0 7.0 - - - +
116L ASN* 5.0 1.0 + - - -
164L THR* 3.0 11.3 - - + +
165L GLY* 1.3 72.6 - - - +
167L GLY* 1.3 66.7 + - - +
169L ARG* 3.2 19.1 - - - +
170L ASN* 3.0 27.9 + - - +
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Residues in contact with GLY 167 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99L ARG* 3.4 24.2 + - - +
162L GLY 3.5 17.9 - - - -
164L THR* 3.0 15.5 + - - +
166L ALA* 1.3 81.3 - - - +
168L ARG* 1.3 61.4 + - - +
170L ASN* 3.7 2.3 - - - +
171L ARG* 3.1 26.9 + - - +
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Residues in contact with ARG 168 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1890 A 2.8 43.2 + - - +
1900 G 4.4 14.8 + - - -
4320 G 4.3 5.4 + - - -
4330 C 2.9 38.9 + - - -
4340 U 5.1 6.1 + - - -
155L GLN* 5.9 1.4 - - - +
162L GLY 3.5 7.8 + - - +
163L LEU* 3.1 33.9 + - - +
164L THR 2.7 19.8 + - - +
165L GLY* 3.9 5.4 - - - +
167L GLY* 1.3 69.9 - - - +
169L ARG* 1.3 64.3 + - + +
171L ARG* 3.3 9.0 + - - +
172L GLY 3.6 0.2 + - - -
173L LEU* 3.1 40.4 + - + +
174L SER 5.2 0.7 - - - -
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Residues in contact with ARG 169 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4000 C 3.7 12.5 + - - +
4300 A 4.8 28.6 + - - -
4310 G 4.4 16.2 + - - -
4320 G 5.4 1.0 + - - -
52L GLN* 5.6 0.4 - - - +
96L ASP* 5.9 0.2 + - - -
98L GLN* 4.1 18.4 + - - +
116L ASN* 4.5 6.9 + - - -
117L SER 5.3 1.6 + - - -
165L GLY* 3.1 27.3 + - - +
166L ALA* 3.2 35.5 - - - +
168L ARG* 1.3 75.9 - - + +
170L ASN* 1.3 58.8 + - - +
171L ARG 3.0 0.2 - - - -
172L GLY* 2.9 20.8 + - - -
173L LEU 4.2 0.4 + - - +
174L SER* 3.7 22.9 + - - +
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Residues in contact with ASN 170 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1570 G 3.5 5.9 + - - -
4000 C 2.9 44.4 + - - +
4010 C 3.1 23.7 + - - +
94L ARG 3.1 17.4 + - - +
95L LYS* 3.6 6.5 - - - +
96L ASP* 3.3 18.0 - - - +
99L ARG* 2.8 30.5 - - - +
166L ALA 3.0 19.5 + - - +
167L GLY 3.7 3.1 - - - +
169L ARG* 1.3 76.8 - - - +
171L ARG* 1.3 57.4 + - - +
172L GLY 3.2 0.9 - - - -
187L LEU* 5.5 0.5 - - - +
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Residues in contact with ARG 171 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1550 C 3.3 10.9 + - - -
1560 C 2.7 57.3 + - - +
1570 G 4.0 15.0 - - - +
1880 C 3.3 18.0 + - - -
1890 A 2.5 31.5 + - - -
3990 C 4.9 1.3 - - - -
4000 C 4.8 1.1 - - - -
99L ARG* 4.1 1.8 - - - +
161L ARG 4.5 0.7 - - - -
162L GLY 3.3 27.4 + - - -
163L LEU* 4.0 2.2 - - - +
167L GLY 3.1 17.1 + - - +
168L ARG* 3.7 7.0 - - - +
169L ARG 3.0 1.4 - - - -
170L ASN* 1.3 76.4 - - - +
172L GLY* 1.3 62.1 + - - +
173L LEU* 3.3 24.9 + - + +
183L THR* 3.4 18.2 - - - +
186L SER* 4.5 3.6 - - - +
187L LEU* 3.7 21.9 - - + +
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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