Contacts of the helix formed by residues 147 - 165 (chain B) in PDB entry 5GQQ
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 SER 147 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58B TRP* 3.9 2.0 - - - -
59B ASP* 3.5 18.6 - - - -
145B PHE 3.9 1.1 + - - -
146B SER* 1.3 76.8 - - - +
148B ALA* 1.3 55.6 + - - +
149B GLN* 3.8 5.7 + - - +
150B LYS* 3.2 23.1 + - - +
151B ASN* 2.8 39.2 + - - -
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Residues in contact with ALA 148 (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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56B MET 5.8 2.0 - - - +
58B TRP* 3.8 28.0 - - + +
59B ASP* 3.6 11.7 + - - +
147B SER* 1.3 73.7 - - - +
149B GLN* 1.3 63.5 + - - +
151B ASN* 3.7 8.9 - - - +
152B GLN* 3.0 25.6 + - - +
174B TYR* 5.6 1.9 + - - -
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Residues in contact with GLN 149 (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 SER* 3.3 6.5 + - - +
148B ALA* 1.3 79.3 - - - +
150B LYS* 1.3 62.7 + - - +
152B GLN* 3.4 21.7 + - - +
153B GLU* 2.9 50.2 + - - +
38C ASP* 3.5 24.5 - - - +
40C SER* 5.8 0.4 - - - -
44C SER* 4.7 9.1 - - - -
204C CL 3.6 10.1 - - + +
50D GLN* 4.2 17.0 + - - -
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Residues in contact with LYS 150 (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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142B PHE* 3.4 28.5 - - + -
143B ASP* 2.7 35.3 + - - +
144B GLY* 4.9 1.0 - - - -
145B PHE 3.6 16.1 + - - +
147B SER* 3.2 24.6 + - - +
149B GLN* 1.3 77.0 - - - +
151B ASN* 1.3 65.9 + - - +
153B GLU* 3.2 9.3 + - - +
154B GLN* 3.0 32.1 + - + +
39C ARG 4.3 6.8 + - - +
40C SER* 3.7 42.6 + - - +
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Residues in contact with ASN 151 (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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58B TRP* 3.4 42.8 - - - +
142B PHE* 3.6 21.8 - - - -
146B SER* 4.1 7.4 + - - -
147B SER 2.8 24.5 + - - +
148B ALA* 3.7 5.6 - - - +
150B LYS* 1.3 70.3 - - - +
152B GLN* 1.3 57.4 + - - +
154B GLN* 3.7 2.4 - - - +
155B LEU* 2.8 33.3 + - - +
174B TYR* 4.6 13.7 + - + +
176B THR* 3.8 15.6 - - + +
192B VAL* 3.9 17.0 - - + +
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Residues in contact with GLN 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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148B ALA 3.0 18.3 + - - +
149B GLN* 3.6 25.1 + - - +
151B ASN* 1.3 77.7 - - - +
153B GLU* 1.3 60.5 + - + +
155B LEU* 3.2 9.3 + - - +
156B LEU* 2.9 43.4 + - + +
174B TYR* 5.4 2.9 + - - +
77C LYS 5.8 0.2 - - - +
78C ALA* 5.7 2.6 - - - +
57D TRP 4.4 8.3 + - - +
59D PRO* 3.8 40.3 - - + +
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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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149B GLN* 2.9 35.7 + - - +
150B LYS* 3.2 4.3 + - - +
152B GLN* 1.3 80.5 - - + +
154B GLN* 1.3 67.3 + - - +
156B LEU* 3.5 6.0 + - - +
157B THR* 2.8 31.9 + - - -
40C SER* 2.5 33.9 + - - +
42C VAL* 3.6 30.8 - - + +
44C SER* 4.3 5.0 - - - -
77C LYS* 4.4 16.5 - - + +
78C ALA 5.5 1.8 - - - +
204C CL 2.7 23.7 - - - +
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Residues in contact with GLN 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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140B ARG* 2.7 49.3 + - - +
141B SER 4.7 0.2 - - - +
142B PHE* 3.9 43.6 - - + +
150B LYS* 3.0 26.3 + - + +
151B ASN 3.9 2.9 - - - +
153B GLU* 1.3 82.6 + - - +
155B LEU* 1.3 60.1 + - - +
157B THR* 3.1 6.3 + - - -
158B LEU* 2.9 25.8 + - - +
192B VAL* 4.2 8.3 - - + -
40C SER 4.5 9.5 + - - -
42C VAL* 4.4 18.4 - - - +
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Residues in contact with LEU 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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151B ASN 2.8 22.0 + - - +
152B GLN* 3.4 8.5 - - - +
154B GLN* 1.3 71.5 - - - +
156B LEU* 1.3 59.5 + - + +
158B LEU* 3.1 5.5 + - + +
159B ALA* 2.8 29.6 + - - +
174B TYR* 3.5 49.6 - - + -
192B VAL* 4.0 24.0 - - + +
193B TRP 4.3 2.0 - - - +
194B LEU* 3.6 33.8 - - + +
57D TRP* 3.8 31.0 - - + +
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Residues in contact with LEU 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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152B GLN* 2.9 30.9 + - + +
153B GLU* 3.8 4.5 - - - +
154B GLN 3.3 0.2 - - - -
155B LEU* 1.3 78.6 - - + +
157B THR* 1.3 61.0 + - - +
159B ALA* 3.4 5.6 + - + +
160B SER* 3.1 22.7 + - - -
163B ARG* 5.4 0.4 + - - +
76C ASN* 3.3 28.0 + - - +
77C LYS* 3.7 24.2 - - - +
78C ALA* 4.7 1.8 - - + +
57D TRP* 3.8 28.0 - - + +
58D THR* 4.4 6.5 - - + -
59D PRO* 3.8 36.8 - - + -
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Residues in contact with THR 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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140B ARG* 3.6 34.3 - - - +
153B GLU 2.8 19.5 + - - -
154B GLN* 3.5 12.7 + - - -
155B LEU 3.1 0.4 - - - -
156B LEU* 1.3 75.4 - - - +
158B LEU* 1.3 66.1 + - - +
160B SER* 3.2 18.1 + - - +
161B ILE* 3.4 13.0 + - + +
75C GLU* 3.6 30.1 - - - +
77C LYS* 3.3 23.1 - - - +
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Residues in contact with LEU 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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37B SER 5.1 0.9 - - - +
38B TYR* 3.8 28.3 - - + -
138B PHE* 3.4 26.5 - - + +
140B ARG* 3.6 22.1 - - + +
154B GLN 2.9 12.9 + - - +
155B LEU* 3.3 8.5 - - + +
157B THR* 1.3 76.8 - - - +
159B ALA* 1.3 62.4 + - - +
161B ILE* 3.1 8.2 + - + +
162B LEU* 2.9 40.6 + - + +
192B VAL* 4.3 15.0 - - + +
194B LEU* 3.7 28.9 - - + +
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Residues in contact with ALA 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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155B LEU 2.8 15.9 + - - +
156B LEU* 3.5 8.7 - - + +
158B LEU* 1.3 77.3 - - - +
160B SER* 1.3 57.1 + - - +
162B LEU* 3.3 3.6 + - - +
163B ARG* 3.0 50.0 + - - +
169B PHE* 4.0 6.3 - - + -
194B LEU* 3.9 10.7 - - + +
57D TRP* 3.7 27.6 - - + -
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Residues in contact with SER 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 LEU 3.1 8.1 + - - -
157B THR 3.2 9.7 + - - -
158B LEU 3.3 0.4 - - - -
159B ALA* 1.3 75.5 - - - +
161B ILE* 1.3 67.0 + - - +
163B ARG* 3.5 12.9 + - - +
164B GLU* 3.3 25.3 + - - +
74C ARG 5.3 0.9 - - - -
75C GLU* 3.6 21.7 - - - +
76C ASN* 3.6 29.4 - - - -
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Residues in contact with ILE 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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37B SER* 4.1 22.7 - - - +
38B TYR* 3.5 31.9 - - + -
140B ARG* 4.1 22.0 - - - +
157B THR* 3.4 20.4 + - + +
158B LEU* 3.1 9.3 + - - +
160B SER* 1.3 83.9 + - - +
162B LEU* 1.3 64.8 + - - +
164B GLU* 3.2 22.8 - - + +
165B ASP* 3.1 24.4 + - - +
75C GLU* 4.9 6.5 - - - +
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Residues in contact with LEU 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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38B TYR* 3.7 26.2 - - + -
138B PHE* 3.5 49.6 - - + -
158B LEU* 2.9 26.1 + - + +
159B ALA 3.7 2.0 - - - +
161B ILE* 1.3 75.6 - - - +
163B ARG* 1.3 61.5 + - - +
165B ASP* 3.2 3.4 + - - +
166B GLY 3.1 4.3 + - - -
167B LYS* 2.8 41.7 + - + +
169B PHE* 3.7 20.9 - - + -
194B LEU* 3.7 29.4 - - + -
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Residues in contact with ARG 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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156B LEU* 5.4 0.4 + - - +
159B ALA* 3.0 42.4 + - - +
160B SER* 3.8 11.3 - - - +
161B ILE 3.3 0.4 - - - -
162B LEU* 1.3 77.0 - - - +
164B GLU* 1.3 58.4 + - - +
166B GLY* 3.1 16.3 + - - -
167B LYS 4.7 5.4 - - - +
169B PHE* 4.1 16.0 - - + -
171B GLU* 3.0 37.8 + - - -
76C ASN* 5.5 6.7 - - - +
57D TRP* 4.3 6.7 - - - -
58D THR* 5.0 3.6 - - - +
140D ARG 5.0 3.0 + - - -
141D GLN* 3.3 26.9 + - - +
142D GLY* 4.9 10.6 + - - +
143D ARG* 5.8 0.6 - - - +
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Residues in contact with GLU 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 SER* 3.3 10.0 + - - +
161B ILE* 3.2 34.3 + - + +
163B ARG* 1.3 77.6 - - - +
165B ASP* 1.3 65.8 + - - +
166B GLY 3.2 3.1 + - - -
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Residues in contact with ASP 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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34B GLN* 4.0 7.1 - - - +
35B PRO* 5.8 0.5 - - - +
38B TYR* 2.6 42.9 + - - +
161B ILE* 3.1 19.0 + - - +
162B LEU 3.2 5.1 + - - +
164B GLU* 1.3 85.4 - - - +
166B GLY* 1.3 62.1 + - - +
167B LYS* 3.2 14.0 + - + +
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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