Contacts of the helix formed by residues 163 - 170 (chain I) in PDB entry 5G04
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 GLU 163 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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161I SER* 3.0 6.1 + - - -
162I ASP* 1.3 81.3 - - - +
164I ILE* 1.3 69.6 + - + +
165I ILE 3.3 1.6 - - - -
166I LYS* 3.3 21.1 + - + +
167I LEU* 3.3 17.5 + - - +
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Residues in contact with ILE 164 (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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94I ASP* 5.2 4.7 - - - +
97I LYS* 4.5 22.9 - - - +
101I LEU* 3.8 33.9 - - + -
154I LYS 4.9 6.7 - - - +
155I ILE* 4.8 22.4 - - + +
158I GLU* 5.4 4.3 - - + -
161I SER* 3.6 30.5 - - - +
163I GLU* 1.3 81.3 - - + +
165I ILE* 1.3 63.6 + - + +
167I LEU* 3.4 11.5 - - + +
168I LEU* 3.4 31.8 + - + +
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Residues in contact with ILE 165 (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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137I LEU* 4.4 20.2 - - + -
138I LEU 4.9 2.0 - - - +
139I LEU* 3.8 48.0 - - + +
140I PRO 3.5 18.4 - - - +
141I LYS* 3.5 40.4 - - + -
155I ILE* 4.8 9.9 - - + -
161I SER 4.3 5.3 + - - +
162I ASP* 4.9 9.4 - - - +
163I GLU* 3.3 0.4 - - - +
164I ILE* 1.3 77.6 - - + +
166I LYS* 1.3 52.9 + - - +
168I LEU* 3.8 1.0 - - - +
169I GLY* 2.8 33.4 + - - -
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Residues in contact with LYS 166 (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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162I ASP 4.4 5.9 + - - +
163I GLU* 3.3 22.5 + - + +
165I ILE* 1.3 79.8 - - - +
167I LEU* 1.3 59.6 + - + +
170I ASP* 2.5 70.5 + - + +
171I VAL* 4.6 0.5 - - - +
383N GLU* 5.7 2.4 + - - -
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Residues in contact with LEU 167 (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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74I ARG* 2.9 27.9 + - - +
78I LYS* 4.6 17.0 - - + +
79I LEU* 3.5 35.9 - - + -
94I ASP* 4.3 26.0 - - - +
96I GLU* 6.2 0.4 - - + -
101I LEU* 4.9 5.6 - - + -
163I GLU 3.3 11.4 + - - +
164I ILE* 3.4 16.2 - - + +
166I LYS* 1.3 83.0 - - + +
168I LEU* 1.3 87.8 + - + +
171I VAL* 3.7 13.7 - - - +
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Residues in contact with LEU 168 (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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74I ARG* 3.8 9.5 + - - +
79I LEU* 3.4 26.9 - - + -
92I LEU* 4.2 7.6 - - + -
101I LEU* 3.9 21.8 - - + -
102I HIS* 5.6 0.9 - - + -
138I LEU* 3.5 12.0 - - + +
139I LEU* 4.1 22.0 - - + -
155I ILE* 5.3 3.4 - - + -
164I ILE* 3.4 35.4 + - + +
165I ILE* 4.0 2.5 - - - +
166I LYS 3.3 0.2 - - - -
167I LEU* 1.3 82.9 - - + +
169I GLY* 1.3 59.5 + - - +
171I VAL* 4.2 4.6 - - - +
174I ASN* 5.2 0.3 - - - +
190I TYR* 3.9 18.4 - - - +
192I MET* 3.7 29.2 - - + -
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Residues in contact with GLY 169 (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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136I ASN 4.9 0.5 - - - +
137I LEU* 5.4 1.2 - - - +
138I LEU* 3.7 27.3 + - - +
165I ILE* 2.8 13.9 + - - -
168I LEU* 1.3 80.4 - - - +
170I ASP* 1.3 62.5 + - - +
171I VAL 3.3 5.2 - - - -
190I TYR* 5.1 0.7 - - - -
253I ARG* 3.1 29.1 + - - -
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Residues in contact with ASP 170 (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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137I LEU* 4.0 20.1 - - - +
165I ILE 4.5 0.5 - - - +
166I LYS* 2.5 75.7 + - + +
168I LEU 3.9 0.2 - - - -
169I GLY* 1.3 73.6 - - - +
171I VAL* 1.3 63.5 + - + +
253I ARG* 4.8 1.3 - - - -
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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