Contacts of the helix formed by residues 138 - 153 (chain B) in PDB entry 6QNW
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 PRO 138 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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126B ARG 5.3 0.4 - - - -
127B GLN* 4.4 19.7 - - - +
137B GLN* 1.3 100.7 - - + +
139B ALA* 1.3 67.3 + - - +
140B ALA* 3.4 3.4 - - + +
141B THR* 3.4 22.2 + - - +
142B ALA* 3.0 22.2 + - - +
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Residues in contact with ALA 139 (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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122B LEU 4.3 5.4 - - - +
123B THR* 3.3 28.5 - - - +
125B GLY* 3.6 21.6 + - - +
126B ARG 3.9 11.5 + - - +
128B THR* 3.7 17.0 - - + +
137B GLN 3.8 0.2 + - - -
138B PRO* 1.3 74.0 - - - +
140B ALA* 1.3 59.8 + - - +
142B ALA* 3.8 1.7 - - - +
143B LEU* 2.9 30.6 + - - +
246B MET* 4.6 4.4 - - + +
249B ARG* 5.5 0.9 - - - +
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Residues in contact with ALA 140 (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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123B THR* 4.3 22.7 + - + +
138B PRO* 3.4 2.5 - - + +
139B ALA* 1.3 78.7 - - - +
141B THR* 1.3 58.9 + - - +
143B LEU* 3.4 7.7 + - - +
144B ALA* 2.9 29.8 + - - +
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Residues in contact with THR 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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133B LEU* 6.2 0.2 - - + -
137B GLN* 3.7 17.9 - - - +
138B PRO* 3.4 27.1 + - - +
139B ALA 3.3 0.2 - - - -
140B ALA* 1.3 76.2 - - - +
142B ALA* 1.3 56.9 + - - +
144B ALA* 3.3 5.9 + - + +
145B ASN* 2.7 51.9 + - - +
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Residues in contact with ALA 142 (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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128B THR* 3.6 17.0 - - - +
129B TYR 5.0 0.4 - - - -
130B ASP* 3.8 28.2 - - + +
137B GLN* 4.2 5.3 - - + +
138B PRO 3.0 18.5 + - - +
139B ALA 3.9 1.1 - - - +
141B THR* 1.3 76.4 - - - +
143B LEU* 1.3 57.3 + - - +
145B ASN* 3.3 10.6 + - - +
146B THR* 2.9 33.7 + - - -
246B MET* 4.2 10.3 - - + -
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Residues in contact with LEU 143 (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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119B VAL* 4.2 11.4 - - + -
122B LEU* 3.6 34.1 - - + -
123B THR* 3.6 30.7 - - + -
139B ALA 2.9 17.9 + - - +
140B ALA* 3.6 7.0 - - - +
142B ALA* 1.3 77.0 - - - +
144B ALA* 1.3 59.5 + - + +
146B THR* 3.4 3.0 + - - -
147B ILE* 2.9 58.4 + - + +
166B PHE* 5.6 2.6 - - + -
246B MET* 3.6 24.8 - - + -
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Residues in contact with ALA 144 (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 ALA 2.9 16.8 + - - +
141B THR* 3.3 7.2 + - + +
143B LEU* 1.3 78.4 - - + +
145B ASN* 1.3 60.6 + - - +
147B ILE* 3.7 7.7 - - - +
148B GLU* 2.9 32.6 + - - +
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Residues in contact with ASN 145 (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 ASP* 3.0 30.9 + - - +
132B THR* 4.0 15.0 + - + +
133B LEU* 4.4 15.6 - - - +
137B GLN* 4.9 2.0 - - - +
141B THR* 2.7 43.8 + - - +
142B ALA* 3.5 3.3 - - - +
144B ALA* 1.3 77.8 - - - +
146B THR* 1.3 57.4 + - - +
148B GLU* 3.4 4.0 + - - +
149B VAL* 2.9 30.8 + - - +
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Residues in contact with THR 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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130B ASP* 4.0 5.4 + - - -
131B TRP* 3.4 25.7 + - + +
132B THR* 4.2 0.9 - - - -
142B ALA 2.9 17.2 + - - -
143B LEU* 3.8 3.8 - - - -
145B ASN* 1.3 76.5 - - - +
147B ILE* 1.3 56.8 + - - +
149B VAL* 3.2 9.7 - - - +
150B PHE* 2.9 60.8 + - + -
166B PHE* 4.2 15.3 - - + -
246B MET* 3.5 18.2 - - + +
247B GLN* 5.0 1.8 - - + +
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Residues in contact with ILE 147 (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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119B VAL* 5.2 7.9 - - + -
143B LEU* 2.9 44.1 + - + +
144B ALA* 3.7 7.2 - - - +
146B THR* 1.3 76.2 - - - +
148B GLU* 1.3 64.1 + - - +
150B PHE* 3.3 5.5 + - - +
151B ARG* 2.9 30.4 + - + +
158B ASN* 3.4 34.8 + - + +
166B PHE* 4.6 10.5 - - + -
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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 ALA 2.9 17.8 + - - +
145B ASN* 4.0 4.0 - - - +
147B ILE* 1.3 81.7 - - - +
149B VAL* 1.3 58.3 + - - +
151B ARG* 3.1 39.3 + - - +
152B SER* 2.9 39.1 + - - +
182B THR* 6.1 0.9 - - - +
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Residues in contact with VAL 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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131B TRP* 3.5 33.0 - - + -
132B THR* 3.8 9.2 - - + +
145B ASN 2.9 17.4 + - - +
146B THR* 3.2 16.4 - - - +
148B GLU* 1.3 77.6 - - - +
150B PHE* 1.3 61.2 + - + +
152B SER* 3.8 6.5 + - - -
153B ASN* 2.9 30.5 + - - +
179B MET* 4.8 1.7 - - + +
180B GLU 3.8 12.8 - - - +
181B ILE* 3.8 35.4 - - + -
182B THR* 4.9 4.3 - - - +
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Residues in contact with PHE 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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131B TRP* 3.8 18.6 - + - -
146B THR* 2.9 40.1 + - + +
147B ILE* 3.7 5.4 - - - +
149B VAL* 1.3 79.7 - - + +
151B ARG* 1.3 59.6 + - - +
153B ASN* 2.9 27.0 + - - +
155B LEU* 3.0 31.4 + - + +
158B ASN* 5.1 4.0 - - - +
166B PHE* 4.2 12.8 - + - -
169B ASP* 4.4 14.1 - - + +
170B VAL* 4.1 27.8 - - + -
173B SER* 4.2 8.3 - - - -
179B MET* 3.7 29.4 - - + -
217B TYR* 3.9 16.6 - - - -
247B GLN* 4.7 2.7 - - - -
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Residues in contact with ARG 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 ILE* 2.9 21.4 + - + +
148B GLU* 3.1 34.6 + - - +
150B PHE* 1.3 72.8 - - - +
152B SER* 1.3 66.9 + - - +
153B ASN 3.0 11.3 - - - +
155B LEU 3.5 8.3 + - - +
156B THR* 3.9 21.3 - - + +
158B ASN* 6.0 1.8 - - - +
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Residues in contact with SER 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 28.8 + - - +
149B VAL* 3.9 9.9 - - - -
150B PHE 3.2 0.2 - - - -
151B ARG* 1.3 81.4 + - - +
153B ASN* 1.3 63.6 + - - +
180B GLU* 5.4 3.1 - - - -
182B THR* 4.2 23.6 + - - +
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Residues in contact with ASN 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 VAL 2.9 18.6 + - - +
150B PHE 2.9 13.1 + - - +
151B ARG* 3.0 12.5 - - - +
152B SER* 1.3 81.1 + - - +
154B GLY* 1.3 58.5 + - - +
155B LEU* 3.0 23.7 + - + -
156B THR* 4.8 2.3 - - - +
176B LYS* 5.0 7.3 - - - +
178B GLU 5.2 2.8 + - - -
179B MET* 3.1 24.2 - - - +
180B GLU* 3.4 37.1 + - - +
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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