Contacts of the helix formed by residues 192 - 199 (chain H) in PDB entry 1CBV
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 192 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142H SER 3.5 8.7 - - - +
143H SER* 4.4 4.0 - - - +
167H LEU* 4.0 16.2 - - + -
168H SER* 4.1 28.9 - - - +
190H THR 4.4 1.3 - - - +
191H VAL* 1.3 96.1 - - + +
193H SER* 1.3 61.9 + - - +
194H SER* 3.1 9.0 - - - +
195H THR* 2.5 35.6 + - + +
196H TRP* 3.3 6.1 + - - +
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Residues in contact with SER 193 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139H THR* 2.8 40.6 + - - +
141H GLY 2.5 30.5 + - - -
142H SER* 2.9 11.5 + - - -
143H SER 4.1 6.4 + - - -
144H VAL* 4.2 5.6 - - - +
191H VAL 3.4 2.6 + - - -
192H PRO* 1.3 67.2 - - - +
194H SER* 1.3 56.4 + - - +
195H THR 3.0 10.2 + - - -
196H TRP* 3.3 20.2 - - - +
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Residues in contact with SER 194 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142H SER 4.7 0.2 + - - -
192H PRO* 3.1 4.4 - - - -
193H SER* 1.3 76.0 - - - +
195H THR* 1.3 67.8 + - - +
199H GLN* 5.0 0.2 + - - -
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Residues in contact with THR 195 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167H LEU* 3.6 25.7 - - + +
191H VAL* 3.7 0.8 - - - +
192H PRO* 2.5 34.2 + - + +
193H SER 3.2 0.4 + - - -
194H SER* 1.3 89.2 - - - +
196H TRP* 1.3 61.5 + - - +
198H SER* 3.3 4.8 + - - -
199H GLN* 2.5 69.0 + - - +
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Residues in contact with TRP 196 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133H ALA* 4.3 4.7 - - + -
134H PRO* 4.0 33.0 - - + -
138H ASP* 4.9 11.2 - - - -
139H THR* 4.1 22.7 - - + +
144H VAL* 4.8 4.7 - - + -
146H LEU* 3.6 39.7 - - + +
191H VAL* 3.9 23.6 - - + -
192H PRO 3.3 5.9 + - - +
193H SER* 3.3 16.6 + - - +
194H SER 5.2 0.2 - - - -
195H THR* 1.3 79.8 - - - +
197H PRO* 1.3 83.0 - - + +
198H SER* 3.5 2.8 + - - -
199H GLN 3.9 15.1 + - - -
201H VAL* 4.2 5.4 - - + +
218H LEU 3.8 26.1 + - - -
219H GLU* 3.8 28.0 - - - -
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Residues in contact with PRO 197 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138H ASP* 4.3 14.6 - - - +
196H TRP* 1.3 112.0 - - + +
198H SER* 1.3 64.5 + - - +
199H GLN 3.3 7.2 + - - +
200H THR* 5.3 0.7 - - - -
219H GLU* 3.3 36.0 - - - +
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Residues in contact with SER 198 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195H THR* 3.3 6.8 + - - -
196H TRP 4.9 1.0 - - - -
197H PRO* 1.3 80.1 - - - +
199H GLN* 1.3 79.6 + - - +
200H THR* 3.6 8.8 + - - +
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Residues in contact with GLN 199 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165H GLY* 5.6 2.7 - - - +
167H LEU* 3.6 28.3 - - + +
194H SER 5.0 0.2 + - - -
195H THR* 2.5 62.1 + - + +
196H TRP* 3.9 17.3 + - - -
197H PRO 3.9 6.2 - - - +
198H SER* 1.3 91.7 - - - +
200H THR* 1.3 59.5 + - - +
201H VAL* 3.3 9.0 + - - +
218H LEU 5.5 0.2 - - - +
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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