Contacts of the helix formed by residues 175 - 183 (chain I) 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 PRO 175 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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117I PHE* 3.6 20.9 - - + -
173I TYR 3.3 8.1 - - - +
174I MET* 1.3 95.5 - - + +
176I VAL* 1.3 60.7 + - - +
177I GLU* 3.3 15.6 + - + +
178I LYS* 3.7 10.6 + - + +
179I LEU* 3.1 22.5 + - - +
449I LYS 6.3 0.4 - - - +
451I GLU* 4.8 7.6 - - + +
452I PHE* 3.9 18.8 - - + -
455I ARG* 3.4 14.8 - - - +
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Residues in contact with VAL 176 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174I MET 3.9 0.8 + - - -
175I PRO* 1.3 71.9 - - - +
177I GLU* 1.3 79.2 + - + +
179I LEU* 3.6 5.6 - - - -
180I ALA* 2.9 28.2 + - - +
199I ASN* 3.3 20.1 - - - +
200I TRP* 3.6 23.3 - - + -
201I GLU* 3.3 38.4 - - + +
205I GLN* 4.4 9.6 - - - +
455I ARG* 4.3 3.6 - - - +
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Residues in contact with GLU 177 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175I PRO* 3.3 12.8 - - - +
176I VAL* 1.3 98.1 + - + +
178I LYS* 1.3 61.2 + - + +
180I ALA* 3.2 5.5 + - - +
181I GLU* 2.9 42.3 + - - +
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Residues in contact with LYS 178 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117I PHE* 3.0 45.1 - - + -
174I MET* 3.8 17.5 - - + -
175I PRO* 3.7 9.7 + - + +
177I GLU* 1.3 75.3 + - + +
179I LEU* 1.3 59.7 + - - +
181I GLU* 3.7 16.4 - - - +
182I ILE* 2.9 42.4 + - + +
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Residues in contact with LEU 179 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114I LEU* 4.3 0.4 - - + -
171I ILE* 3.7 22.9 - - + -
174I MET* 3.8 19.4 - - + -
175I PRO 3.1 20.0 + - - +
176I VAL* 3.5 10.3 - - - +
177I GLU 3.1 0.2 - - - -
178I LYS* 1.3 77.2 - - - +
180I ALA* 1.3 56.6 + - - +
183I PHE* 2.9 57.3 + - + +
200I TRP* 3.5 42.0 - - + +
205I GLN* 4.5 15.5 - - + +
208I MET* 3.7 13.5 - - + -
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Residues in contact with ALA 180 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176I VAL 2.9 17.5 + - - +
177I GLU* 3.9 4.3 - - - +
179I LEU* 1.3 76.6 - - - +
181I GLU* 1.3 60.3 + - + +
183I PHE 2.9 17.6 - - - +
184I SER* 4.7 1.9 - - - -
185I VAL* 3.8 29.0 - - + +
199I ASN* 4.6 6.7 - - - +
200I TRP* 4.4 7.0 - - + +
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Residues in contact with GLU 181 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177I GLU* 2.9 27.5 + - - +
178I LYS* 3.7 20.2 + - - +
180I ALA* 1.3 80.7 - - + +
182I ILE* 1.3 64.2 + - + +
183I PHE 4.1 1.6 - - - +
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Residues in contact with ILE 182 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107I GLN* 5.0 0.3 - - - +
109I ASP* 5.0 3.8 - - - +
110I GLN* 3.3 41.6 + - - +
113I GLN* 3.3 50.8 - - + +
114I LEU 4.7 1.6 - - - +
117I PHE* 5.6 0.4 - - + -
174I MET* 3.7 27.4 - - + -
178I LYS* 2.9 27.5 + - + +
179I LEU* 4.4 0.7 - - - +
181I GLU* 1.3 82.5 - - + +
183I PHE* 1.3 74.1 - - + +
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Residues in contact with PHE 183 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105I TYR* 3.5 24.0 - + - +
106I LEU* 5.4 5.4 - - + -
110I GLN* 3.2 56.5 - - + +
114I LEU* 3.6 39.0 - - + -
171I ILE* 4.2 7.4 - - + -
179I LEU* 2.9 40.1 + - + +
180I ALA 2.9 19.8 - - - +
181I GLU 4.0 2.1 - - - +
182I ILE* 1.3 87.2 - - + +
184I SER* 1.3 68.1 + - - +
200I TRP* 5.0 1.6 - - + -
208I MET* 4.8 3.8 - - + -
212I PHE* 4.5 15.9 - + - -
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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