Contacts of the strand formed by residues 193 - 197 (chain A) in PDB entry 2CG2
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 GLN 193 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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163A ARG* 2.9 9.2 + - - +
164A THR* 3.3 20.2 + - - +
165A VAL 2.9 25.8 + - - +
190A GLY* 5.1 7.0 - - - +
191A ALA 5.9 0.2 - - - -
192A VAL* 1.3 76.6 - - - +
194A ILE* 1.3 64.6 + - - +
195A ILE* 3.6 22.0 - - + +
254A THR* 3.6 11.2 - - - +
255A ARG* 5.2 4.2 - - - +
264A LEU* 6.0 0.2 - - - +
266A LEU* 4.2 14.9 - - - +
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Residues in contact with ILE 194 (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 VAL* 3.1 15.5 - - + +
167A TYR* 3.4 41.1 - - + +
178A VAL* 4.8 4.5 - - + -
182A VAL* 4.8 1.8 - - + -
187A VAL* 3.7 31.2 - - + -
192A VAL* 4.4 5.6 - - + -
193A GLN* 1.3 78.2 - - - +
195A ILE* 1.3 62.0 + - - +
251A LEU* 3.8 22.4 - - + -
252A ALA 3.7 14.1 - - - +
253A PRO* 3.5 17.3 - - + +
254A THR* 2.7 35.2 + - + +
255A ARG 3.0 9.2 + - - +
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Residues in contact with ILE 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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164A THR* 3.6 21.1 - - + -
165A VAL 2.8 7.1 + - - -
166A ILE* 3.2 14.2 - - + +
167A TYR* 2.8 27.5 + - - +
193A GLN* 3.6 28.9 - - + +
194A ILE* 1.3 77.1 - - - +
196A ALA* 1.3 64.8 + - - +
255A ARG* 3.2 27.6 - - + +
257A ILE* 3.4 35.9 - - + -
264A LEU* 4.6 7.2 - - + -
266A LEU* 4.6 8.5 - - + -
273A PHE* 4.5 7.0 - - + -
285A MET* 4.5 5.6 - - + -
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Residues in contact with ALA 196 (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 TYR* 3.9 9.0 - - + -
195A ILE* 1.3 77.6 - - - +
197A PRO* 1.4 73.1 - - + +
200A PHE* 3.7 31.6 - - + -
253A PRO* 3.8 17.9 - - + -
255A ARG 3.0 6.1 + - - -
256A LEU* 3.2 5.1 - - + -
257A ILE* 2.8 23.9 + - - +
285A MET* 3.8 6.3 - - - -
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Residues in contact with PRO 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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167A TYR 3.2 18.8 - - - +
168A SER 4.0 2.5 - - - +
169A HIS* 4.4 1.3 - - - -
196A ALA* 1.4 88.1 - - + +
198A ALA* 1.3 68.9 + - - +
200A PHE* 3.1 25.2 + - + +
256A LEU* 3.7 2.0 - - - +
257A ILE 3.9 1.8 - - - +
275A ASN* 3.2 27.6 - - - +
283A ALA* 3.5 13.2 - - + +
284A GLU* 3.5 33.7 - - - +
285A MET* 3.7 12.7 - - + -
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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