Contacts of the helix formed by residues 151 - 165 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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113B PHE* 4.1 7.3 - - - -
149B ASN* 3.4 21.7 + - + +
150B GLN* 1.3 75.6 - - - +
152B LYS* 1.3 54.9 + - - +
153B GLU* 2.9 14.3 - - - +
154B LEU* 2.6 49.6 + - - +
155B GLU* 3.0 7.2 + - - +
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Residues in contact with LYS 152 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150B GLN 4.1 0.8 + - - -
151B THR* 1.3 71.6 - - - +
153B GLU* 1.3 61.0 + - - +
154B LEU 3.0 0.2 - - - -
155B GLU* 3.0 24.4 + - + +
156B GLU* 3.0 33.0 + - + +
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Residues in contact with GLU 153 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113B PHE* 3.2 35.1 - - + -
151B THR* 2.9 13.4 - - - +
152B LYS* 1.3 79.2 - - - +
154B LEU* 1.3 59.9 + - - +
156B GLU* 3.7 18.7 - - - +
157B LYS* 3.7 3.6 + - - +
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Residues in contact with LEU 154 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113B PHE* 3.4 29.6 - - + -
116B LEU* 4.6 10.8 - - + +
117B ALA* 4.1 28.0 - - + +
146B LEU* 4.1 32.8 - - + -
147B ALA* 4.4 15.5 - - + -
149B ASN* 5.2 2.5 - - - +
150B GLN* 4.1 16.4 - - - +
151B THR* 2.6 26.9 + - - +
153B GLU* 1.3 76.6 - - - +
155B GLU* 1.3 62.1 + - - +
156B GLU 3.0 5.5 + - - -
157B LYS* 3.2 4.0 + - - +
158B VAL* 3.2 25.2 + - + +
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Residues in contact with GLU 155 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141B VAL* 3.6 23.0 - - + +
142B SER* 2.9 37.2 - - - +
150B GLN* 3.5 30.2 + - - +
151B THR 3.0 2.1 + - - +
152B LYS* 3.0 44.6 + - + +
154B LEU* 1.3 76.9 - - + +
156B GLU* 1.3 64.7 + - - +
158B VAL* 3.8 5.4 + - - +
159B MET* 3.3 33.1 + - + +
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Residues in contact with GLU 156 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138B VAL* 4.2 26.3 - - - +
152B LYS* 3.0 25.6 + - + +
153B GLU* 3.7 12.8 - - - +
154B LEU 3.0 1.0 + - - -
155B GLU* 1.3 77.7 - - - +
157B LYS* 1.3 68.3 + - - +
159B MET* 3.0 21.2 + - - +
160B GLU* 3.1 11.4 + - - +
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Residues in contact with LYS 157 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113B PHE* 4.3 13.7 - - + -
114B ALA* 5.9 3.6 - - - +
117B ALA* 3.7 23.1 - - + -
153B GLU 3.7 7.4 + - - +
154B LEU 3.2 7.9 + - - +
156B GLU* 1.3 78.9 - - - +
158B VAL* 1.3 62.6 + - - +
160B GLU* 3.2 46.8 + - - +
161B LEU* 3.2 30.6 + - + +
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Residues in contact with VAL 158 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117B ALA* 3.5 35.0 - - - +
120B GLY* 4.0 2.9 - - - -
121B SER* 3.9 15.6 - - - +
124B ILE* 3.9 23.8 - - + -
141B VAL* 3.9 11.2 - - + -
146B LEU* 3.9 21.8 - - + -
154B LEU* 3.2 20.8 + - + +
155B GLU* 3.9 5.8 - - - +
156B GLU 3.1 0.6 - - - -
157B LYS* 1.3 78.8 - - - +
159B MET* 1.3 56.8 + - - +
161B LEU* 3.8 3.3 + - - +
162B HIS* 3.0 26.4 + - + +
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Residues in contact with MET 159 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138B VAL* 3.5 21.5 - - - +
139B ASP* 3.3 13.5 - - - -
140B TYR* 3.2 64.6 - - + +
141B VAL* 3.2 28.3 - - + +
142B SER 4.6 0.4 - - - +
155B GLU* 3.3 17.0 + - + +
156B GLU* 3.0 16.5 + - - +
158B VAL* 1.3 74.9 - - - +
160B GLU* 1.3 65.8 + - - +
162B HIS* 4.3 0.4 - - - -
163B LYS* 2.9 43.8 + - - +
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Residues in contact with GLU 160 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156B GLU 3.1 10.8 + - - +
157B LYS* 3.2 41.7 + - - +
159B MET* 1.3 80.4 - - - +
161B LEU* 1.3 74.8 + - - +
163B LYS* 3.0 15.0 + - - +
164B SER* 3.1 12.7 + - - -
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Residues in contact with LEU 161 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114B ALA 5.4 0.4 - - - +
117B ALA* 3.7 36.1 - - + +
118B LEU* 3.9 12.8 - - + +
121B SER* 3.5 18.6 - - - +
157B LYS* 3.2 29.3 + - + +
158B VAL 4.0 0.2 - - - +
160B GLU* 1.3 93.7 - - + +
162B HIS* 1.3 63.9 + - - +
164B SER* 2.9 25.1 + - - -
165B TYR* 3.1 27.6 + - + +
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Residues in contact with HIS 162 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121B SER* 4.0 6.4 - - - +
124B ILE* 3.5 27.4 - - + +
125B GLN* 2.9 39.2 + - - +
128B LEU* 4.7 0.2 - - - +
129B GLY 3.2 13.0 - - - -
131B TYR* 3.5 24.0 - - + +
135B LEU* 3.6 10.5 - - - +
140B TYR* 2.8 35.7 - + - +
158B VAL* 3.0 20.5 + - + +
159B MET* 3.8 2.7 - - - +
161B LEU* 1.3 75.9 - - - +
163B LYS* 1.3 61.6 + - - +
165B TYR* 3.2 27.9 + - - +
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Residues in contact with LYS 163 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131B TYR* 3.5 63.0 + - + +
137B GLY 6.0 0.2 + - - -
138B VAL* 5.1 13.1 - - - +
140B TYR* 4.1 13.4 - - - +
159B MET* 2.9 36.6 + - - +
160B GLU* 3.0 7.4 + - - +
162B HIS* 1.3 76.5 - - - +
164B SER* 1.3 61.4 + - - +
165B TYR 3.3 6.2 - - - +
166B ARG* 4.4 7.6 - - - +
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Residues in contact with SER 164 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160B GLU* 3.1 10.5 + - - -
161B LEU* 2.9 17.1 + - - -
163B LYS* 1.3 74.5 - - - +
165B TYR* 1.3 80.0 + - - +
166B ARG* 3.5 6.2 + - - +
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Residues in contact with TYR 165 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118B LEU* 3.4 19.6 - - - +
121B SER* 3.0 40.7 + - - -
122B TYR* 3.5 25.4 + + - -
125B GLN* 3.6 21.5 + - + -
130B ASP* 4.5 0.4 - - - -
131B TYR* 5.0 1.9 + - - +
161B LEU* 3.1 27.0 + - + +
162B HIS* 3.2 20.5 + - - +
163B LYS* 3.3 2.3 - - - +
164B SER* 1.3 89.6 + - - +
166B ARG* 1.3 67.7 + - - +
168B MET* 3.2 32.3 - - + -
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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