Contacts of the helix formed by residues 184 - 192 (chain C) in PDB entry 6GYS
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 SER 184 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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105C TYR* 3.5 15.0 + - - -
183C PHE* 1.3 78.8 - - - +
185C VAL* 1.3 67.2 + - - +
186C TYR* 3.3 8.5 + - - +
187C PRO* 3.3 31.2 - - - +
188C LEU* 4.0 3.5 - - - +
200C TRP* 3.3 7.5 - - - +
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Residues in contact with VAL 185 (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* 1.3 72.2 + - - +
186C TYR* 1.3 68.8 + - + +
188C LEU* 3.4 4.0 + - - +
189C HIS* 2.9 52.1 + - + +
196C LYS 3.4 26.5 - - - +
198C LEU 3.7 15.5 - - - +
199C ASN* 4.8 6.3 - - - +
200C TRP* 3.5 39.9 - - + +
204C MET* 5.6 0.4 - - + -
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Residues in contact with TYR 186 (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* 3.2 6.0 - - - +
185C VAL* 1.3 84.7 - - + +
187C PRO* 1.4 66.7 - - + +
188C LEU 3.2 1.1 - - - -
190C GLU* 2.9 13.5 + - - +
196C LYS* 2.3 80.1 + - + +
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Residues in contact with PRO 187 (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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101C PHE* 4.8 2.3 - - - -
105C TYR* 4.5 15.7 - - + -
184C SER* 3.3 31.9 - - - +
186C TYR* 1.4 90.1 - - + +
188C LEU* 1.3 62.2 + - - +
190C GLU* 4.1 4.8 - - + +
191C TYR* 3.3 21.3 + - - +
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Residues in contact with LEU 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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101C PHE* 3.6 27.1 - - + -
102C TRP* 3.6 16.8 - - + -
105C TYR* 3.3 45.3 - - + +
184C SER 4.0 1.1 - - - +
185C VAL 3.4 6.9 + - - +
186C TYR 3.2 0.4 - - - -
187C PRO* 1.3 73.6 - - - +
189C HIS* 1.3 52.6 + - - +
190C GLU 3.1 3.4 - - - -
191C TYR* 2.8 5.9 + - - -
192C LEU* 2.5 41.7 + - + +
200C TRP* 3.5 29.4 - - + -
204C MET* 3.7 21.5 - - + -
208C MET* 4.0 8.7 - - - -
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Residues in contact with HIS 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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185C VAL* 2.9 42.1 + - + +
188C LEU* 1.3 73.8 - - - +
190C GLU* 1.3 57.0 + - - +
192C LEU* 4.1 9.1 - - + +
193C GLY* 3.1 20.6 + - - -
194C SER* 3.3 29.0 + - - +
195C ASN* 2.7 28.1 + - - -
196C LYS* 3.3 27.7 + - + -
198C LEU* 3.5 20.6 - - + +
204C MET* 2.8 41.3 - - + +
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Residues in contact with GLU 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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186C TYR 2.9 17.9 + - - +
187C PRO* 4.1 6.1 - - + +
189C HIS* 1.3 77.8 - - - +
191C TYR* 1.3 65.6 + - - +
193C GLY* 3.3 9.5 + - - -
196C LYS* 3.4 16.2 - - - +
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Residues in contact with TYR 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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94C THR* 5.9 0.3 - - - +
97C GLU* 4.1 5.2 + - - +
98C GLU* 3.0 43.0 + - - -
101C PHE* 3.4 56.2 - + + +
187C PRO 3.3 12.2 + - - +
188C LEU 2.8 6.9 + - - +
190C GLU* 1.3 82.4 - - - +
192C LEU* 1.3 69.1 + - + +
193C GLY* 3.4 0.3 + - - -
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Residues in contact with LEU 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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98C GLU* 5.1 1.3 - - - +
101C PHE* 4.5 0.2 - - + -
102C TRP* 4.0 28.9 - - + -
188C LEU* 2.5 35.9 + - + +
189C HIS* 4.1 9.2 - - + -
191C TYR* 1.3 89.0 - - + +
193C GLY* 1.3 61.0 + - - +
194C SER* 3.2 19.2 + - - +
204C MET* 3.9 26.7 - - + -
207C VAL* 4.4 19.1 - - + -
211C ASN* 5.1 2.2 - - - +
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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