Contacts of the helix formed by residues 139 - 144 (chain C) in PDB entry 1GG3
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 ASP 139 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136C HIS 3.7 2.1 - - - +
137C GLY* 3.2 21.2 + - - -
138C VAL* 1.3 80.0 + - - +
140C TYR* 1.3 62.2 + - - +
141C VAL* 2.3 23.6 + - - +
142C SER* 2.5 33.3 + - - -
155C GLU* 4.5 8.5 - - - +
159C MET* 3.5 8.3 - - - +
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Residues in contact with TYR 140 (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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128C LEU* 3.6 21.1 - - + +
131C TYR* 3.8 17.0 - + - -
135C LEU* 3.1 43.1 - - + +
136C HIS 3.5 13.9 - - - +
137C GLY 3.7 7.0 - - - -
139C ASP* 1.3 82.8 + - - +
141C VAL* 1.3 68.0 + - + -
142C SER* 3.0 9.1 + - - -
143C ASP* 4.2 6.1 + - - +
144C PHE* 4.2 12.1 - - - -
159C MET* 3.2 39.3 + - + +
162C HIS* 2.8 40.1 - + - +
163C LYS* 4.3 3.0 - - - -
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Residues in contact with VAL 141 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124C ILE* 3.5 35.9 - - + -
139C ASP 2.3 14.4 + - - +
140C TYR* 1.3 87.1 - - + +
142C SER* 1.3 58.1 + - - +
143C ASP 3.2 6.8 + - - -
144C PHE* 3.6 18.7 + - + +
146C LEU* 3.7 19.1 - - + -
150C GLN* 4.8 1.7 - - - +
155C GLU* 4.0 18.6 - - + +
158C VAL* 4.5 5.6 - - + -
159C MET* 3.2 35.2 - - + +
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Residues in contact with SER 142 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139C ASP* 2.5 31.5 + - - -
140C TYR* 3.0 5.3 + - - -
141C VAL* 1.3 72.1 - - - +
143C ASP* 1.3 76.3 + - - +
144C PHE 3.6 0.2 - - - -
150C GLN* 5.0 4.9 + - - -
152C LYS* 6.3 0.7 - - - -
155C GLU* 3.6 21.7 - - - +
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Residues in contact with ASP 143 (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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140C TYR 4.2 4.5 + - - +
141C VAL 3.2 0.8 - - - -
142C SER* 1.3 97.3 + - - +
144C PHE* 1.3 71.8 + - + +
145C LYS* 3.7 13.1 + - - +
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Residues in contact with PHE 144 (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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19A LYS* 4.3 19.5 - - - -
101C ARG* 4.4 13.0 - - - +
123C THR* 5.1 0.7 - - + -
124C ILE* 3.8 17.0 - - + -
127C GLU* 3.6 40.6 - - + -
128C LEU* 3.7 37.2 - - + -
140C TYR 4.2 17.0 - - - -
141C VAL* 3.6 9.5 + - - +
142C SER 3.6 0.2 - - - -
143C ASP* 1.3 87.4 - - + +
145C LYS* 1.3 53.5 + - - +
146C LEU* 2.9 27.2 - - + +
150C GLN* 2.4 25.2 - - - +
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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