Contacts of the helix formed by residues 168 - 176 (chain B) in PDB entry 1CGP
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 168 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167B ILE* 1.3 78.6 - - - +
169B ARG* 1.3 55.4 + - - +
170B GLN* 3.9 12.6 - - + +
171B GLU* 2.8 56.7 + - + +
172B ILE* 3.0 15.1 + - - +
200B GLY* 6.1 0.2 - - - -
23C G 2.8 26.0 + - - +
24C T 2.6 27.4 + - - -
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Residues in contact with ARG 169 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167B ILE* 4.3 8.1 + - - +
168B THR* 1.3 71.5 + - - +
170B GLN* 1.3 56.9 + - - +
172B ILE* 3.2 4.4 + - - +
173B GLY* 2.8 25.3 + - - -
180B ARG* 3.7 25.5 - - + +
183B VAL* 3.5 19.6 - - + +
184B GLY* 4.1 7.6 - - - +
187B LEU* 3.7 30.4 - - + +
198B ALA* 3.8 22.0 - - - +
199B HIS* 4.6 2.8 - - - +
200B GLY* 3.5 30.9 - - - +
202B THR* 4.7 6.7 + - - -
24C T 3.1 37.9 + - - +
25C G 3.7 22.1 + - - +
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Residues in contact with GLN 170 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57B LYS* 4.8 12.7 + - - +
168B THR* 3.1 7.9 + - + +
169B ARG* 1.3 75.5 - - - +
171B GLU* 1.3 61.9 + - - +
173B GLY* 3.4 1.6 + - - -
174B GLN* 3.0 37.9 + - - +
180B ARG* 3.9 30.5 - - + +
23C G 2.9 57.1 + - - +
24C T 2.9 21.8 + - - +
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Residues in contact with GLU 171 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60B ILE* 3.1 24.1 - - - +
63B TYR* 2.8 26.7 + - - +
89B LYS* 5.3 6.1 - - - +
167B ILE* 3.6 20.4 - - + +
168B THR* 2.8 36.4 + - + +
170B GLN* 1.3 70.7 - - - +
172B ILE* 1.4 65.1 + - - +
174B GLN* 3.0 20.7 + - - +
175B ILE* 2.9 27.8 + - - +
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Residues in contact with ILE 172 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143B ILE* 4.1 25.4 - - + -
146B THR* 4.4 9.4 - - + -
147B LEU* 3.8 27.6 - - + -
150B LEU* 4.8 5.2 - - + -
167B ILE* 3.7 31.4 - - + -
168B THR 3.0 10.6 + - - +
169B ARG* 3.7 7.2 - - - +
171B GLU* 1.4 74.2 - - - +
173B GLY* 1.3 63.5 + - - +
175B ILE* 3.0 10.1 + - - +
176B VAL* 2.8 27.2 + - + +
183B VAL* 3.8 22.7 - - + -
187B LEU* 4.4 15.9 - - + -
202B THR* 5.6 1.3 - - - +
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Residues in contact with GLY 173 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57B LYS* 5.9 2.7 - - - -
169B ARG 2.8 12.4 + - - -
170B GLN* 3.7 4.5 - - - -
172B ILE* 1.3 75.0 - - - +
174B GLN* 1.3 56.6 + - - +
177B GLY* 2.7 30.5 + - - -
178B CYS* 3.3 29.2 + - - -
179B SER 5.0 1.1 - - - -
180B ARG 5.2 0.2 - - - -
183B VAL* 3.5 14.7 - - - +
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Residues in contact with GLN 174 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50B LEU* 4.7 1.2 - - - +
57B LYS* 4.4 24.2 - - + +
58B GLU* 3.8 44.5 + - - +
59B MET* 3.2 14.4 - - - +
60B ILE* 3.1 36.9 + - + +
170B GLN* 3.0 23.0 + - - +
171B GLU* 3.0 28.1 + - - +
173B GLY* 1.3 75.1 - - - +
175B ILE* 1.3 61.2 + - - +
177B GLY* 5.2 0.8 - - - -
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Residues in contact with ILE 175 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59B MET* 3.5 3.8 - - - +
60B ILE* 4.1 20.4 - - + +
63B TYR* 3.9 25.6 - - + +
130B LYS* 3.1 39.8 + - - +
146B THR* 3.9 37.9 - - + +
150B LEU* 4.4 12.8 - - + -
167B ILE* 4.7 2.2 - - + -
171B GLU 2.9 20.0 + - - +
172B ILE* 3.0 10.5 + - - +
174B GLN* 1.3 76.8 - - - +
176B VAL* 1.3 63.7 + - - +
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Residues in contact with VAL 176 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59B MET* 4.2 1.1 - - - -
134B LEU* 3.6 10.4 - - - +
139B VAL* 3.7 15.0 - - + -
142B ARG* 2.7 59.5 + - + +
143B ILE* 3.7 22.0 - - + +
146B THR* 3.9 19.5 - - - +
172B ILE* 2.8 20.6 + - + +
173B GLY 3.8 1.6 - - - +
175B ILE* 1.3 76.8 - - + +
177B GLY* 1.3 54.3 + - - +
178B CYS* 3.4 26.5 - - - -
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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