Contacts of the helix formed by residues 140 - 158 (chain B) in PDB entry 4GQS
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 140 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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133B ASN* 3.0 14.2 + - - -
134B PHE* 3.3 38.4 - - - -
138B LYS 3.1 4.2 + - - -
139B ARG* 1.3 77.5 - - - +
141B ILE* 1.3 67.6 + - - +
142B GLU* 3.1 21.0 + - - +
143B ASP* 3.3 13.9 + - - +
144B ARG* 3.3 20.4 + - - +
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Residues in contact with ILE 141 (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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130B THR 4.9 0.4 - - - +
131B LEU* 3.9 16.8 - - + +
132B ARG 3.5 14.1 - - - +
133B ASN* 2.6 31.3 + - - +
136B MET* 3.5 32.3 - - - -
140B SER* 1.3 69.1 + - - +
142B GLU* 1.3 66.5 + - - +
144B ARG* 3.0 9.8 + - + +
145B VAL* 2.8 31.6 + - + +
181B ILE* 4.0 20.6 - - + -
440B LEU* 3.5 30.5 - - + -
443B MET* 3.9 8.7 - - + -
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Residues in contact with GLU 142 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133B ASN* 3.8 6.7 + - - +
134B PHE* 6.1 0.7 - - - -
140B SER* 3.1 11.0 + - - +
141B ILE* 1.3 79.0 - - - +
143B ASP* 1.3 52.3 + - - +
145B VAL* 3.1 1.6 + - - +
146B GLN* 2.7 60.9 + - + +
338B CYS* 3.6 8.3 - - - +
339B MET* 2.7 46.1 + - + +
340B GLN 4.2 1.4 + - - -
443B MET* 3.7 25.6 - - + -
447B LEU* 4.6 1.8 - - + -
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Residues in contact with ASP 143 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139B ARG* 2.6 39.5 + - + +
140B SER* 3.3 19.4 + - - +
141B ILE 3.2 0.4 - - - -
142B GLU* 1.3 78.8 - - - +
144B ARG* 1.3 62.8 + - - +
146B GLN* 4.0 5.8 - - - +
147B GLU* 2.8 30.5 + - - +
150B ARG* 5.4 4.5 + - - -
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Residues in contact with ARG 144 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136B MET* 3.5 34.7 - - - +
137B GLY* 5.3 2.2 - - - +
139B ARG* 3.1 83.2 + - - +
140B SER 3.3 8.4 + - - +
141B ILE* 3.0 11.6 + - + +
143B ASP* 1.3 76.2 - - - +
145B VAL* 1.3 65.3 + - + +
147B GLU* 3.8 2.6 + - - +
148B GLU* 3.4 17.8 + - - +
177B VAL* 4.7 9.6 - - + +
180B SER* 3.2 38.8 + - - +
181B ILE* 4.0 21.5 - - + -
184B GLN* 4.2 6.5 + - - +
186B ARG* 5.9 0.9 - - - -
260B PRO 5.4 0.8 + - - -
261B ARG 3.6 18.2 + - - -
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Residues in contact with VAL 145 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141B ILE* 2.8 29.5 + - + +
142B GLU 3.3 5.8 - - - +
144B ARG* 1.3 74.3 - - + +
146B GLN* 1.3 61.2 + - - +
148B GLU* 2.8 22.5 + - - +
149B ALA* 3.0 10.0 + - - +
177B VAL* 4.0 22.0 - - + -
440B LEU* 4.3 3.6 - - + -
443B MET* 3.4 28.9 - - + -
444B GLU* 4.2 23.1 - - + -
447B LEU* 4.1 19.5 - - + -
448B PHE* 4.1 9.5 - - + -
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Residues in contact with GLN 146 (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 GLU* 2.7 49.2 + - - +
143B ASP* 4.0 4.8 - - - +
145B VAL* 1.3 72.7 - - - +
147B GLU* 1.3 64.2 + - - +
149B ALA* 2.9 21.2 + - - +
150B ARG* 3.0 23.2 + - - +
336B SER* 3.9 7.3 + - - +
337B PRO 3.0 24.3 - - - +
338B CYS* 3.9 10.8 - - - +
447B LEU* 3.3 20.9 - - + -
451B PHE* 3.6 13.8 - - + -
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Residues in contact with GLU 147 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139B ARG* 2.6 37.0 + - - +
143B ASP* 2.8 25.4 + - - +
144B ARG 4.0 1.3 - - - +
146B GLN* 1.3 72.6 - - - +
148B GLU* 1.3 59.4 + - - +
150B ARG* 3.2 36.6 + - - +
151B CYS* 3.1 30.0 + - - -
186B ARG* 3.3 33.4 + - - +
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Residues in contact with GLU 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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144B ARG 3.4 11.3 + - - +
145B VAL 2.8 13.8 + - - +
147B GLU* 1.3 78.4 - - - +
149B ALA* 1.3 63.1 + - - +
151B CYS* 3.2 4.5 + - - +
152B LEU* 2.9 21.3 + - - +
172B CYS 4.0 1.6 - - - +
173B ALA* 3.4 23.1 - - + +
176B ASN* 3.3 22.7 + - - +
177B VAL* 3.9 11.2 - - + -
186B ARG* 2.7 49.5 + - - +
189B TYR* 3.1 19.9 + - - -
448B PHE* 4.0 8.5 - - + -
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Residues in contact with ALA 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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145B VAL 3.0 6.5 + - - +
146B GLN* 2.9 15.6 + - - +
148B GLU* 1.3 76.1 - - - +
150B ARG* 1.3 63.1 + - - +
152B LEU* 3.0 5.8 + - - +
153B VAL* 2.9 25.5 + - - +
447B LEU* 5.0 3.4 - - + -
448B PHE* 3.6 27.5 - - + -
451B PHE* 3.3 35.6 - - + +
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Residues in contact with ARG 150 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143B ASP* 5.4 4.8 + - - -
146B GLN* 3.0 17.8 + - + +
147B GLU* 3.2 48.8 - - - +
149B ALA* 1.3 75.8 - - - +
151B CYS* 1.3 60.1 + - - +
153B VAL* 3.0 9.7 + - - +
154B GLU* 2.9 30.6 + - - +
451B PHE* 4.3 13.4 - - + -
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Residues in contact with CYS 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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147B GLU* 3.1 28.9 - - - -
148B GLU* 3.2 8.6 + - - +
150B ARG* 1.3 80.1 - - - +
152B LEU* 1.3 61.9 + - - +
154B GLU* 3.9 7.8 - - - +
155B GLU* 3.1 30.8 + - + +
186B ARG* 3.6 44.2 - - - +
189B TYR* 4.6 4.0 - - + +
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Residues in contact with LEU 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 GLU 2.9 12.4 + - - +
149B ALA* 3.1 10.5 - - - +
151B CYS* 1.3 73.8 - - - +
153B VAL* 1.3 60.6 + - + +
155B GLU* 2.9 7.4 + - - +
156B LEU* 2.8 37.9 + - + +
169B ILE* 3.4 37.7 - - + +
170B LEU* 4.7 11.0 - - + -
173B ALA* 4.3 12.8 - - + -
189B TYR* 4.1 13.9 + - - +
306B LEU* 5.8 0.2 - - + -
448B PHE* 3.8 32.8 - - + -
451B PHE* 6.3 1.1 - - + -
452B ILE* 4.2 22.2 - - + -
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Residues in contact with VAL 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 ALA 2.9 17.2 + - - +
150B ARG* 3.4 7.9 - - - +
152B LEU* 1.3 76.5 - - + +
154B GLU* 1.3 56.2 + - - +
156B LEU* 2.7 31.2 + - + +
157B ARG* 2.9 30.8 + - - +
451B PHE* 3.7 38.4 - - + +
452B ILE* 5.0 2.9 - - + +
455B ASN* 3.7 18.4 - - - +
456B PHE* 3.7 19.7 - - + -
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Residues in contact with GLU 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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150B ARG 2.9 18.8 + - - +
151B CYS* 3.9 9.0 - - - +
153B VAL* 1.3 74.8 - - - +
155B GLU* 1.3 58.2 + - + +
157B ARG* 3.8 25.6 + - - +
158B LYS* 2.7 54.2 + - - +
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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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151B CYS* 3.1 18.6 + - + +
152B LEU* 2.9 12.2 + - - +
154B GLU* 1.3 76.5 - - + +
156B LEU* 1.3 64.2 + - - +
157B ARG 3.3 0.4 - - - -
158B LYS* 3.4 35.3 - - - +
159B THR 3.9 2.3 + - - -
168B PHE* 6.1 0.3 - - - -
169B ILE* 4.3 24.2 - - + +
189B TYR* 3.6 40.6 - - + +
190B LYS* 4.2 19.3 + - - -
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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 LEU* 2.8 22.1 + - + +
153B VAL* 2.7 11.8 + - - +
155B GLU* 1.3 76.5 - - - +
157B ARG* 1.3 60.0 + - - +
158B LYS 3.1 0.2 - - - -
159B THR* 2.9 35.4 + - - +
166B PRO* 6.4 0.9 - - + -
169B ILE* 4.5 21.5 - - + -
170B LEU* 6.1 3.8 - - + -
452B ILE* 3.6 37.5 - - + -
456B PHE* 3.5 27.9 - - + -
487B PHE* 3.6 41.7 - - + -
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Residues in contact with ARG 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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153B VAL* 2.9 36.0 + - - +
154B GLU* 3.8 34.8 + - - +
156B LEU* 1.3 73.5 - - - +
158B LYS* 1.3 57.1 + - + +
159B THR 2.9 10.5 + - - -
160B LYS* 2.9 20.6 + - - +
455B ASN* 4.1 19.6 + - - +
456B PHE* 3.8 19.0 - - + -
489B PRO* 4.4 23.3 - - + +
490B ILE 5.6 0.6 - - - +
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Residues in contact with LYS 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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154B GLU* 2.7 48.8 + - - +
155B GLU* 3.4 32.8 - - - +
157B ARG* 1.3 77.6 - - + +
159B THR* 1.3 60.4 + - - +
160B LYS* 3.2 21.3 - - - -
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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