Contacts of the helix formed by residues 169 - 184 (chain A) 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 169 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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167A SER 3.3 6.5 + - - +
168A MET* 1.3 75.0 - - - +
170A PRO* 1.3 77.4 - - + +
171A ALA* 3.9 5.8 + - - +
172A GLN* 2.7 51.8 + - - +
173A ALA* 2.9 21.4 + - - +
70B PRO* 5.0 15.9 - - + -
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Residues in contact with PRO 170 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125A GLN 5.7 1.1 - - - +
126A SER* 3.8 32.4 + - - +
168A MET 4.5 0.9 - - - +
169A THR* 1.3 89.2 - - - +
171A ALA* 1.3 63.1 + - - +
173A ALA* 3.3 2.0 + - + +
174A ASP* 2.9 30.2 + - - +
68B GLY* 4.5 13.5 - - - +
69B VAL* 3.7 21.1 - - - +
70B PRO* 4.0 26.0 - - + -
71B TRP* 6.1 1.6 - - + -
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Residues in contact with ALA 171 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90A ASP* 2.9 34.1 - - + +
93A ARG* 5.5 1.9 - - - +
169A THR* 3.3 6.8 + - - +
170A PRO* 1.3 81.1 - - - +
172A GLN* 1.3 58.8 + - + +
174A ASP* 3.3 9.5 + - - +
175A LEU* 3.0 30.5 + - - +
68B GLY* 3.9 16.1 + - - +
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Residues in contact with GLN 172 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167A SER 3.8 5.5 + - - -
168A MET* 3.4 19.8 - - - +
169A THR* 2.7 52.1 + - - +
171A ALA* 1.3 73.4 - - + +
173A ALA* 1.3 66.2 + - - +
174A ASP 3.0 1.3 - - - -
175A LEU* 3.0 17.4 + - - +
176A GLU* 3.0 17.4 + - + +
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Residues in contact with ALA 173 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122A TYR* 3.5 29.9 - - - +
125A GLN* 3.6 19.7 - - + -
126A SER* 3.2 21.8 - - - +
168A MET* 3.8 16.0 - - + +
169A THR 2.9 14.6 + - - +
170A PRO* 3.7 1.8 - - + +
172A GLN* 1.3 76.5 - - - +
174A ASP* 1.3 61.9 + - - +
176A GLU 3.4 0.3 + - - -
177A PHE* 3.1 17.8 + - - +
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Residues in contact with ASP 174 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90A ASP 4.8 1.2 - - - +
93A ARG* 4.7 11.0 - - + -
94A TYR* 3.6 33.2 + - - +
97A CYS* 3.7 26.0 - - - +
123A THR* 6.0 0.2 - - - -
126A SER* 3.0 21.8 + - - -
170A PRO* 2.9 21.7 + - - +
171A ALA* 3.4 8.8 - - - +
173A ALA* 1.3 78.2 - - - +
175A LEU* 1.3 57.2 + - - +
177A PHE* 3.1 6.1 + - - +
178A LEU* 2.8 34.2 + - - +
68B GLY* 5.3 3.5 - - - -
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Residues in contact with LEU 175 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84A PRO* 5.9 0.2 - - + -
85A ALA* 3.9 18.6 - - + +
93A ARG* 3.2 44.0 - - + +
171A ALA 3.0 12.1 + - - +
172A GLN* 3.0 11.2 + - - +
174A ASP* 1.3 75.2 - - - +
176A GLU* 1.3 61.3 + - - +
178A LEU* 4.3 6.7 - - + -
179A GLU* 2.9 57.6 + - + +
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Residues in contact with GLU 176 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122A TYR* 3.3 42.6 + - + +
168A MET* 5.0 5.8 - - - -
172A GLN* 3.0 13.9 + - + +
173A ALA 3.8 4.3 - - - +
175A LEU* 1.3 80.3 - - - +
177A PHE* 1.3 65.0 + - - +
179A GLU* 3.6 13.1 + - - +
180A ASN* 2.8 35.7 + - - -
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Residues in contact with PHE 177 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97A CYS* 3.9 18.2 - - + -
100A LEU* 4.0 27.1 - - + -
101A ARG* 4.0 20.4 - - + -
104A ILE* 4.0 20.6 - - + -
119A LEU* 3.2 54.4 - - + +
122A TYR* 3.7 13.2 - - + -
123A THR* 3.4 22.9 - - - -
173A ALA 3.1 15.0 + - - +
174A ASP* 3.3 11.7 - - - +
176A GLU* 1.3 78.6 - - - +
178A LEU* 1.3 62.2 + - + +
180A ASN 3.2 1.6 + - - -
181A ALA* 2.8 27.2 + - + -
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Residues in contact with LEU 178 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84A PRO* 3.8 27.0 - - + +
93A ARG* 3.4 45.5 - - + +
96A LEU* 4.4 8.3 - - + -
97A CYS* 3.3 26.2 - - - +
100A LEU* 3.7 28.0 - - + -
174A ASP 2.8 20.8 + - - +
175A LEU* 3.9 9.2 - - + +
177A PHE* 1.3 73.1 - - + +
179A GLU* 1.3 60.7 + - - +
180A ASN 3.0 2.2 - - - -
181A ALA* 4.0 1.5 - - - +
182A LYS* 2.8 33.8 + - - +
187A TYR* 5.6 0.3 - - - -
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Residues in contact with GLU 179 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83A ASP* 4.2 0.3 - - - +
84A PRO* 5.5 0.8 - - - +
85A ALA* 3.4 19.1 + - - +
175A LEU* 2.9 49.4 + - + +
176A GLU* 4.0 18.2 - - - +
177A PHE 3.4 0.2 - - - -
178A LEU* 1.3 73.7 - - - +
180A ASN* 1.3 61.4 + - - +
182A LYS* 2.7 45.5 + - - +
183A LYS* 3.1 24.7 - - + +
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Residues in contact with ASN 180 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115A THR* 5.4 4.8 - - + +
118A LEU* 3.1 33.8 - - + +
119A LEU* 3.7 13.7 - - + -
122A TYR* 3.6 11.9 + - - -
176A GLU* 2.8 24.2 + - - +
177A PHE 3.2 8.7 + - - +
178A LEU 3.0 0.6 - - - -
179A GLU* 1.3 80.2 - - - +
181A ALA* 1.3 65.8 + - - +
182A LYS 3.3 0.2 - - - -
183A LYS* 3.3 36.1 + - - +
184A LEU* 3.6 9.1 + - - +
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Residues in contact with ALA 181 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100A LEU* 3.6 29.8 - - + -
109A LEU* 4.8 9.6 - - + -
119A LEU* 3.9 6.0 - - + +
177A PHE* 2.8 28.4 + - + +
178A LEU* 4.0 2.0 - - - +
180A ASN* 1.3 70.7 - - - +
182A LYS* 1.3 68.2 + - - +
184A LEU* 2.9 30.7 + - + +
187A TYR* 3.6 13.8 - - + +
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Residues in contact with LYS 182 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82A PRO 2.9 29.6 - - - +
83A ASP* 3.3 24.3 + - + +
84A PRO* 3.7 12.6 - - + -
178A LEU 2.8 20.5 + - - +
179A GLU* 2.7 41.1 + - - +
181A ALA* 1.3 76.7 - - - +
183A LYS* 1.3 66.7 + - + +
184A LEU 3.6 5.9 + - - +
187A TYR* 4.0 22.2 - - + -
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Residues in contact with LYS 183 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179A GLU* 3.1 22.7 - - + +
180A ASN* 3.3 24.1 + - - +
181A ALA 3.0 0.6 - - - -
182A LYS* 1.3 86.3 - - + +
184A LEU* 1.3 68.0 + - - +
185A SER* 3.4 2.3 + - - -
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Residues in contact with LEU 184 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109A LEU* 3.2 42.2 - - + -
110A PRO 4.2 4.9 - - - +
111A CYS* 3.7 35.4 - - + -
115A THR* 3.9 20.6 - - + +
119A LEU* 4.5 5.2 - - + -
180A ASN 3.6 7.8 + - - +
181A ALA* 2.9 24.3 + - - +
182A LYS 3.6 2.3 - - - +
183A LYS* 1.3 77.7 - - - +
185A SER* 1.3 63.9 + - - +
187A TYR* 3.4 16.5 + - + +
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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