Contacts of the helix formed by residues 151 - 164 (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 THR 151 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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113C PHE* 4.6 3.5 - - - -
149C ASN* 4.3 20.6 + - + +
150C GLN* 1.3 78.7 - - - +
152C LYS* 1.3 55.5 + - - +
153C GLU* 3.8 16.2 + - - +
154C LEU* 2.4 48.3 + - - +
155C GLU* 3.2 5.6 + - - +
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Residues in contact with LYS 152 (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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142C SER* 6.3 1.0 - - - -
151C THR* 1.3 70.6 - - - +
153C GLU* 1.3 63.8 + - + +
154C LEU 2.9 0.3 + - - -
155C GLU* 2.9 30.5 + - - +
156C GLU* 2.9 43.0 + - + +
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Residues in contact with GLU 153 (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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113C PHE* 3.1 23.7 - - + -
151C THR* 2.7 15.2 + - - +
152C LYS* 1.3 76.3 - - + +
154C LEU* 1.3 60.7 + - - +
156C GLU* 3.9 7.6 + - - +
157C LYS* 3.6 13.3 + - - +
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Residues in contact with LEU 154 (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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113C PHE* 3.2 29.1 - - + +
116C LEU* 3.4 34.3 - - + +
117C ALA* 3.7 18.6 - - + -
146C LEU* 4.7 7.9 - - + -
147C ALA* 3.8 25.8 - - + -
149C ASN* 5.0 2.2 - - - +
150C GLN* 4.1 16.8 - - + -
151C THR* 2.4 31.0 + - - +
153C GLU* 1.3 72.1 - - - +
155C GLU* 1.3 67.0 + - - +
156C GLU 3.1 1.0 + - - -
157C LYS* 3.3 3.5 + - - +
158C VAL* 3.2 29.6 + - + +
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Residues in contact with GLU 155 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138C VAL 5.5 0.5 - - - +
139C ASP* 4.5 9.4 - - - +
141C VAL* 4.0 14.1 - - + +
142C SER* 3.6 32.2 - - - +
146C LEU* 5.9 0.9 - - - -
150C GLN* 3.6 28.9 + - - +
151C THR 4.0 5.6 - - - +
152C LYS* 2.9 45.2 + - - +
154C LEU* 1.3 77.4 - - + +
156C GLU* 1.3 68.6 + - - +
158C VAL* 3.2 9.1 + - - +
159C MET* 2.9 34.0 + - + +
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Residues in contact with GLU 156 (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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138C VAL* 3.1 33.5 - - - +
152C LYS* 2.9 43.4 + - + +
153C GLU* 3.9 7.6 - - - +
155C GLU* 1.3 75.8 - - - +
157C LYS* 1.3 55.0 + - - +
158C VAL 2.5 17.1 + - - -
159C MET* 2.6 27.9 + - - +
160C GLU* 2.7 17.9 + - + -
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Residues in contact with LYS 157 (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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113C PHE* 4.2 12.3 - - + -
114C ALA* 6.1 1.8 - - - +
117C ALA* 3.8 23.1 - - + -
153C GLU 3.6 9.9 + - - +
154C LEU 3.3 8.6 + - - +
156C GLU* 1.3 78.5 - - - +
158C VAL* 1.3 56.6 + - - +
160C GLU* 3.7 25.2 + - - +
161C LEU* 3.0 50.0 + - + +
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Residues in contact with VAL 158 (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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116C LEU 4.7 0.2 - - - +
117C ALA* 3.5 29.4 - - - +
120C GLY* 3.3 33.2 - - - +
121C SER* 3.4 5.7 - - - +
124C ILE* 4.5 6.3 - - + -
141C VAL* 4.5 7.9 - - + -
146C LEU* 3.7 23.8 - - + -
154C LEU* 3.2 22.7 - - + +
155C GLU* 3.3 7.4 - - - +
156C GLU 2.5 4.8 + - - -
157C LYS* 1.3 72.2 - - - +
159C MET* 1.3 56.3 + - - +
161C LEU* 2.9 5.4 + - - +
162C HIS* 2.6 36.1 + - - +
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Residues in contact with MET 159 (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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138C VAL* 3.2 44.9 - - + +
139C ASP* 3.5 13.2 - - - +
140C TYR* 3.2 43.3 - - + +
141C VAL* 3.2 25.4 - - + -
155C GLU* 2.9 18.4 + - + +
156C GLU* 2.6 27.3 + - - +
158C VAL* 1.3 71.2 - - - +
160C GLU* 1.3 64.3 + - - +
162C HIS* 2.9 15.0 + - - +
163C LYS* 2.9 26.4 + - - +
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Residues in contact with GLU 160 (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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156C GLU* 2.7 22.9 + - + +
157C LYS* 3.7 31.9 + - - +
159C MET* 1.3 74.8 - - - +
161C LEU* 1.3 61.8 + - - +
163C LYS* 3.6 21.1 + - - +
164C SER* 3.9 6.1 + - - -
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Residues in contact with LEU 161 (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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114C ALA 5.6 0.4 - - - +
117C ALA* 4.3 3.1 - - + +
118C LEU* 4.2 28.0 - - + +
121C SER* 3.9 9.0 - - - -
157C LYS* 3.0 51.3 + - + +
158C VAL 2.9 4.5 + - - +
160C GLU* 1.3 76.6 - - + +
162C HIS* 1.3 63.8 + - - +
164C SER* 2.9 30.3 + - - +
165C TYR* 3.0 30.7 - - + +
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Residues in contact with HIS 162 (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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121C SER* 4.5 2.2 - - - +
124C ILE* 3.1 39.0 + - + +
125C GLN* 2.9 35.9 + - - +
128C LEU* 4.5 0.8 - - - +
129C GLY 3.0 12.0 + - - -
131C TYR* 3.6 25.4 - + - +
135C LEU* 4.0 9.5 - - - +
140C TYR* 2.8 30.4 - + - +
158C VAL 2.6 15.5 + - - +
159C MET* 2.9 9.6 + - - +
161C LEU* 1.3 71.1 - - - +
163C LYS* 1.3 56.7 + - - +
165C TYR* 2.9 37.4 + - - +
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Residues in contact with LYS 163 (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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131C TYR* 3.2 64.8 + - + +
137C GLY 4.7 4.6 + - - -
138C VAL* 4.5 23.4 - - - +
140C TYR* 4.3 11.6 - - - +
159C MET* 2.9 22.9 + - - +
160C GLU* 3.7 13.2 - - - +
161C LEU 3.2 0.2 - - - -
162C HIS* 1.3 75.4 - - - +
164C SER* 1.3 55.7 + - - +
165C TYR 3.1 3.6 + - - -
166C ARG* 4.3 17.5 + - - +
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Residues in contact with SER 164 (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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160C GLU 3.9 5.4 + - - -
161C LEU* 2.9 25.3 + - - +
162C HIS 3.0 1.6 + - - -
163C LYS* 1.3 76.8 - - - +
165C TYR* 1.3 71.5 + - - +
166C ARG* 3.9 3.8 + - - -
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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