Contacts of the helix formed by residues 152 - 169 (chain B) in PDB entry 3GA5
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 HIS 152 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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70B PRO* 4.6 6.7 - - + +
91B ASN 3.9 9.0 - - - -
92B LYS* 3.6 18.1 - - + +
149B GLU* 3.0 45.7 + - + +
150B PRO 3.2 2.4 + - - -
151B GLY* 1.3 76.5 - - - +
153B PRO* 1.4 76.7 - - + +
154B ASP* 3.1 40.0 + - + +
155B ALA* 3.0 7.5 + - + +
156B GLU* 3.0 23.1 + - - +
183B TRP* 3.4 17.4 - + - -
401B RGG 2.7 27.6 + - - -
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Residues in contact with PRO 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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70B PRO* 4.4 10.5 - - + -
92B LYS 5.2 0.2 - - - -
93B GLU* 3.7 43.7 - - + +
112B SER* 3.9 13.5 - - - +
151B GLY 3.5 8.5 - - - +
152B HIS* 1.4 93.6 - - + +
154B ASP* 1.3 55.8 + - - +
156B GLU* 3.6 5.7 + - + +
157B ALA* 3.0 31.9 + - - +
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Residues in contact with ASP 154 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91B ASN 3.7 1.7 - - - +
93B GLU 5.8 0.7 + - - -
107B TYR* 5.1 0.5 + - - -
112B SER* 2.6 30.6 + - - -
152B HIS* 3.1 21.6 + - + -
153B PRO* 1.3 77.2 - - - +
155B ALA* 1.3 59.8 + - - +
158B ARG* 2.9 56.7 + - - +
183B TRP* 4.3 3.8 - - + -
295B TYR* 3.5 10.2 + - - -
401B RGG 2.5 43.8 + - - +
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Residues in contact with ALA 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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147B LYS* 4.2 8.5 - - + -
148B GLY* 3.7 18.8 - - - +
149B GLU 3.3 26.0 - - - +
152B HIS* 3.0 7.5 + - - +
154B ASP* 1.3 75.1 - - - +
156B GLU* 1.3 62.9 + - - +
159B THR* 2.8 32.3 + - - -
183B TRP* 3.9 9.6 - - + -
210B ASN* 3.3 18.6 - - - +
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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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147B LYS* 3.1 34.1 + - - +
149B GLU 4.4 0.2 - - - +
150B PRO* 3.7 2.1 - - - +
151B GLY* 2.8 35.0 + - - +
152B HIS 3.0 19.5 + - - +
153B PRO* 4.0 5.6 - - + +
155B ALA* 1.3 75.9 - - - +
157B ALA* 1.3 56.9 + - - +
159B THR* 3.9 1.6 - - - -
160B THR* 2.9 36.4 + - - +
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Residues in contact with ALA 157 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112B SER* 3.6 33.2 - - - -
113B LYS* 3.8 6.3 - - + +
153B PRO 3.0 20.5 + - - +
154B ASP 4.4 0.4 - - - +
156B GLU* 1.3 74.5 - - - +
158B ARG* 1.3 60.9 + - - +
160B THR* 4.4 1.1 - - - -
161B TYR* 2.8 47.1 + - + +
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Residues in contact with ARG 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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112B SER 4.4 2.9 - - - +
115B SER* 3.1 25.3 + - - +
116B GLY* 4.1 13.1 - - - +
119B GLN* 4.5 6.0 - - - +
154B ASP* 2.9 35.9 + - - +
157B ALA* 1.3 77.0 - - - +
159B THR* 1.3 59.3 + - - +
162B VAL* 3.2 31.7 + - - +
183B TRP* 3.7 12.9 - - - -
210B ASN* 2.9 44.9 + - - +
235B VAL* 3.6 17.5 - - + +
256B ASN* 3.8 3.8 - - - +
295B TYR* 2.9 28.1 + - - -
401B RGG 2.8 43.6 + - - -
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Residues in contact with THR 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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145B LEU* 3.6 21.8 - - + +
147B LYS* 3.6 19.3 - - - +
155B ALA 2.8 22.2 + - - -
156B GLU* 3.9 2.7 - - - -
158B ARG* 1.3 76.0 - - - +
160B THR* 1.3 66.2 + - - +
162B VAL* 3.5 17.1 - - - +
163B VAL* 3.8 11.2 - - + +
175B GLN* 5.8 0.7 - - - +
178B LEU* 4.0 14.8 - - + -
210B ASN* 3.1 22.3 + - - +
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Residues in contact with THR 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* 2.9 24.4 + - - +
157B ALA* 3.9 2.7 - - - -
159B THR* 1.3 82.1 - - - +
161B TYR* 1.3 78.0 + - + +
163B VAL* 3.5 4.4 + - - +
164B LYS* 3.1 42.0 + - + +
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Residues in contact with TYR 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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113B LYS* 3.5 55.4 - - + +
116B GLY* 3.9 6.2 - - - +
117B VAL* 4.1 15.4 - - + +
157B ALA* 2.8 37.8 + - + +
160B THR* 1.3 88.2 - - + +
162B VAL* 1.3 65.2 + - - +
164B LYS* 4.3 29.3 - - + +
165B GLU* 2.9 27.4 + - - +
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Residues in contact with VAL 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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116B GLY* 3.5 11.5 + - - +
119B GLN* 3.4 20.2 - - - +
120B GLY* 3.7 16.0 - - - +
123B ILE* 3.7 27.4 - - + -
145B LEU* 4.3 6.1 - - + -
158B ARG 3.2 23.4 + - - +
159B THR 3.5 11.0 - - - +
161B TYR* 1.3 75.8 - - - +
163B VAL* 1.3 73.7 + - + +
166B LEU* 3.2 29.1 + - + +
208B ILE* 4.1 22.9 - - + -
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Residues in contact with VAL 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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143B TYR* 3.4 33.7 - - + +
145B LEU* 5.2 1.6 - - + -
159B THR* 3.8 13.9 - - + +
160B THR* 3.5 7.5 + - - +
162B VAL* 1.3 87.0 - - + +
164B LYS* 1.3 68.5 + - + +
166B LEU* 3.2 9.9 + - + +
167B ASN* 2.9 33.3 + - - +
173B THR* 3.6 22.2 - - + +
208B ILE* 5.6 0.9 - - + -
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Residues in contact with LYS 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 THR* 3.1 37.5 + - + +
161B TYR* 3.4 27.7 + - + +
163B VAL* 1.3 78.8 - - + +
165B GLU* 1.3 58.6 + - - +
167B ASN* 3.2 8.4 + - - +
168B ASP* 2.8 49.5 + - - +
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Residues in contact with GLU 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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117B VAL* 3.5 39.2 - - + +
120B GLY* 4.1 6.3 - - - -
121B ASP* 2.5 40.5 - - - +
161B TYR 2.9 18.1 + - - +
162B VAL 4.0 2.9 - - - +
164B LYS* 1.3 75.7 - - - +
166B LEU* 1.3 65.0 + - - +
168B ASP* 3.0 17.6 + - - +
169B LYS* 3.0 38.5 + - - +
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Residues in contact with LEU 166 (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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120B GLY* 3.5 24.0 - - - +
123B ILE* 3.9 22.7 - - + -
124B ALA* 3.8 21.3 - - + +
141B ILE* 4.3 10.1 - - + -
143B TYR* 6.1 0.2 - - + -
162B VAL 3.2 18.4 + - - +
163B VAL* 3.5 8.7 - - + +
165B GLU* 1.3 76.9 - - - +
167B ASN* 1.3 64.6 + - - +
169B LYS* 2.9 16.4 + - - +
171B ILE* 3.2 30.6 + - + +
173B THR* 3.9 27.4 - - + -
208B ILE* 4.5 17.5 - - + -
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Residues in contact with ASN 167 (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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163B VAL* 2.9 28.1 + - - +
164B LYS* 3.6 9.1 - - - +
166B LEU* 1.3 74.4 - - - +
168B ASP* 1.3 60.0 + - - +
170B GLY* 3.0 20.8 + - - -
171B ILE 2.9 22.9 + - - -
172B GLN* 4.2 1.9 - - - +
173B THR* 3.1 28.6 + - - +
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Residues in contact with ASP 168 (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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164B LYS* 2.8 38.2 + - - +
165B GLU* 3.0 21.8 + - - +
167B ASN* 1.3 75.7 - - - +
169B LYS* 1.3 59.9 + - + +
170B GLY 3.2 3.1 + - - -
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Residues in contact with LYS 169 (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 ASP* 2.7 34.9 + - - +
124B ALA* 3.6 31.9 - - + -
165B GLU* 3.4 20.8 + - + +
166B LEU 2.9 10.1 + - - +
168B ASP* 1.3 78.2 + - + +
170B GLY* 1.3 59.4 - - - +
171B ILE* 3.2 12.0 + - + +
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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