Contacts of the helix formed by residues 187 - 194 (chain C) in PDB entry 8GSS
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 187 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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185C ALA 2.9 9.5 - - - +
186C ARG* 1.4 82.0 - - + +
188C LYS* 1.3 66.7 + - + +
190C LYS* 3.4 9.2 + - + +
191C ALA* 3.1 24.3 + - - +
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Residues in contact with LYS 188 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22C ALA* 3.6 20.6 - - - +
23C ASP* 3.6 28.6 + - - +
24C GLN 4.6 0.9 - - - -
25C GLY* 3.8 17.9 - - - +
186C ARG 3.4 0.4 - - - -
187C PRO* 1.3 81.0 - - + +
189C LEU* 1.3 63.1 + - - +
191C ALA* 3.5 6.9 + - - +
192C PHE* 3.1 22.5 + - - +
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Residues in contact with LEU 189 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19C MET* 3.8 31.6 - - + +
23C ASP* 3.5 29.4 + - + +
153C TYR* 4.5 14.4 - - + -
156C LEU* 3.7 24.7 - - + -
183C LEU* 3.3 27.4 - - + +
184C SER* 4.6 2.7 - - - +
186C ARG* 2.9 10.4 + - + +
188C LYS* 1.3 75.5 - - - +
190C LYS* 1.3 61.5 + - - +
192C PHE* 3.0 7.6 + - + +
193C LEU* 2.8 46.2 + - + +
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Residues in contact with LYS 190 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184C SER 3.3 17.4 + - - +
185C ALA* 3.5 32.3 + - - +
186C ARG 2.8 15.4 + - - +
187C PRO* 3.7 8.3 - - + +
189C LEU* 1.3 71.3 - - - +
191C ALA* 1.3 64.1 + - - +
193C LEU* 3.2 7.5 + - - +
194C ALA* 3.1 25.7 + - + +
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Residues in contact with ALA 191 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187C PRO 3.1 14.4 + - - +
188C LYS* 3.6 7.9 - - - +
190C LYS* 1.3 80.6 - - - +
192C PHE* 1.3 61.7 + - - +
194C ALA* 3.3 5.5 + - - +
195C SER* 3.1 20.8 + - - -
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Residues in contact with PHE 192 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15C ALA 4.9 0.2 - - - -
18C ARG* 3.6 34.8 - - + -
19C MET* 4.0 21.5 - - + -
22C ALA* 3.5 30.5 - - + -
28C TRP* 3.9 20.6 - + - -
188C LYS 3.1 8.4 + - - +
189C LEU* 3.0 9.2 + - + +
191C ALA* 1.3 77.0 - - - +
193C LEU* 1.3 66.2 + - + +
195C SER* 2.7 31.4 + - - -
197C GLU* 4.0 22.2 - - + -
198C TYR* 3.5 40.0 - + + +
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Residues in contact with LEU 193 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19C MET* 3.9 20.9 - - + -
156C LEU* 5.3 0.7 - - + -
160C LEU* 4.7 11.9 - - + -
184C SER* 4.2 32.3 - - - +
189C LEU* 2.8 37.8 + - + +
190C LYS* 3.2 5.1 + - - +
192C PHE* 1.3 73.4 - - + +
194C ALA* 1.3 57.9 + - - +
198C TYR* 3.3 57.8 - - + +
199C VAL* 3.5 7.6 - - - +
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Residues in contact with ALA 194 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190C LYS* 3.1 17.1 + - + +
191C ALA* 3.8 5.8 - - - +
192C PHE 3.1 0.8 - - - -
193C LEU* 1.3 77.1 - - - +
195C SER* 1.3 64.8 + - - +
196C PRO* 3.9 1.9 - - - +
199C VAL* 3.6 11.4 - - - +
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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