Contacts of the helix formed by residues 194 - 198 (chain A) in PDB entry 1CM8
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 PRO 194 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192A ARG 3.8 0.6 - - - -
193A ALA* 1.3 87.0 - - + +
195A GLU* 1.3 65.7 + - - +
197A ILE* 2.9 22.7 + - - +
198A LEU* 3.0 23.0 + - + +
210A TRP* 3.7 29.2 - - + -
235A LEU* 3.8 23.8 - - + +
238A ILE* 4.0 11.0 - - + -
239A MET* 4.7 3.1 - - + -
294A LEU* 3.5 38.1 - - + +
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Residues in contact with GLU 195 (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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193A ALA* 3.3 17.3 - - - +
194A PRO* 1.3 74.0 - - + +
196A VAL* 1.3 59.9 + - - +
197A ILE 2.9 5.6 - - - -
198A LEU* 4.1 5.1 - - + +
199A ASN* 2.8 49.8 + - + +
203A TYR* 3.9 21.0 - - + +
204A THR 5.2 0.4 + - - +
206A THR* 4.5 1.2 + - - -
207A VAL* 3.4 15.6 + - - +
294A LEU 4.3 5.5 - - - +
296A ALA* 4.2 15.8 - - + +
299A ARG* 2.4 43.6 + - - -
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Residues in contact with VAL 196 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184A GLY 3.3 22.3 - - - +
185A PTR 5.2 1.1 - - + -
186A VAL* 3.8 15.9 - - + +
187A VAL* 4.6 7.9 - - + -
192A ARG* 3.6 34.3 - - + +
193A ALA 3.0 22.2 + - - +
194A PRO 3.0 0.4 + - - -
195A GLU* 1.3 78.9 - - - +
197A ILE* 1.3 59.7 + - + +
199A ASN 4.4 0.2 - - - -
200A TRP* 3.5 25.7 - - + -
201A MET 4.5 1.7 + - - -
203A TYR* 4.4 13.0 - - + -
207A VAL* 4.4 21.1 - - + -
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Residues in contact with ILE 197 (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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185A PTR 5.2 3.4 - - + -
192A ARG* 4.3 15.3 - - + +
193A ALA 5.5 0.4 - - - +
194A PRO 2.9 8.4 + - - +
196A VAL* 1.3 89.6 - - + +
198A LEU* 1.3 65.2 + - - +
199A ASN 3.1 1.9 + - - -
200A TRP* 3.4 25.1 + - + +
231A HIS* 3.3 51.6 - - + +
232A LEU* 4.4 11.0 - - + -
234A GLN* 5.8 0.7 - - + -
235A LEU* 3.9 24.5 - - + -
255A SER* 4.2 3.9 + - - +
257A GLU* 4.8 7.0 - - - +
258A ALA* 3.8 18.6 - - + +
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Residues in contact with LEU 198 (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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194A PRO* 3.0 25.0 + - + +
195A GLU* 4.3 5.4 - - + +
197A ILE* 1.3 76.8 - - - +
199A ASN* 1.3 58.4 + - + +
200A TRP 3.8 1.4 + - - -
235A LEU* 3.6 26.5 - - + -
239A MET* 4.0 22.2 - - + -
245A PRO* 4.6 8.7 - - + -
249A PHE* 4.6 20.6 - - + -
253A LEU* 3.7 28.6 - - + +
254A GLN* 5.4 1.6 + - - +
255A SER* 4.7 9.9 + - - -
258A ALA* 3.9 14.1 - - + -
262A MET* 3.8 20.2 - - + -
294A LEU* 5.6 3.8 - - + -
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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