Contacts of the helix formed by residues 139 - 151 (chain B) in PDB entry 4WB7
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 GLN 139 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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109B PHE* 3.4 43.0 - - + -
134B VAL* 2.9 23.8 + - + +
137B LEU* 3.0 26.5 + - + +
138B LYS* 1.3 83.4 + - - +
140B ILE* 1.3 60.1 + - - +
141B GLU 3.5 1.6 - - - -
142B HIS* 2.7 40.8 + - + +
143B THR* 2.8 35.6 + - - +
241B GLY 4.8 0.2 - - - +
242B PHE* 3.6 11.5 - - - -
22J ILE 5.3 0.6 + - - -
23J HIS* 4.6 7.3 + - - +
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Residues in contact with ILE 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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134B VAL* 3.6 6.5 - - - +
135B VAL* 3.9 36.6 - - + +
138B LYS* 3.6 3.7 - - - -
139B GLN* 1.3 78.1 - - - +
141B GLU* 1.3 65.9 + - - +
143B THR* 3.8 1.6 - - - -
144B LEU* 3.0 36.0 + - + +
401B GLU* 3.7 49.1 - - + +
402B PHE* 4.1 12.2 - - + -
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Residues in contact with GLU 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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138B LYS 5.4 0.6 + - - -
139B GLN 3.5 0.2 - - - -
140B ILE* 1.3 80.8 - - - +
142B HIS* 1.3 70.0 + - + +
144B LEU* 3.3 9.8 + - + +
145B ASN* 2.9 43.8 + - - +
244B LYS* 4.1 22.9 + - - +
252B TPO 4.6 6.5 + - - -
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Residues in contact with HIS 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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138B LYS 5.1 4.0 - - - -
139B GLN* 2.7 43.9 + - + +
140B ILE 3.2 0.4 - - - -
141B GLU* 1.3 87.1 - - + +
143B THR* 1.3 58.2 + - - +
145B ASN* 3.5 12.7 + - - +
146B GLU* 2.9 28.9 + - - +
220B ARG* 3.9 9.0 + - - -
241B GLY 3.3 21.8 - - - +
242B PHE* 3.7 20.0 - + - -
243B ALA 5.8 0.2 - - - -
252B TPO 2.8 49.7 + - + +
254B CYS* 4.4 4.5 - - + -
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Residues in contact with THR 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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129B LEU* 3.6 29.8 - - + +
134B VAL* 3.5 18.2 - - + +
139B GLN* 2.8 28.9 + - - +
140B ILE 3.8 2.5 - - - -
142B HIS* 1.3 74.4 - - - +
144B LEU* 1.3 67.1 + - - +
146B GLU* 3.4 11.9 + - - +
147B LYS* 3.3 22.5 + - - +
171B LEU* 3.7 23.3 - - + -
173B MET* 4.7 1.3 - - + +
402B PHE* 4.7 2.0 - - + -
405B PHE* 4.4 8.2 - - + -
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Residues in contact with LEU 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 ILE* 3.0 32.0 + - + +
141B GLU* 3.7 8.5 - - + +
143B THR* 1.3 77.7 - - - +
145B ASN* 1.3 62.6 + - - +
147B LYS* 3.6 3.7 + - - +
148B ARG* 3.1 26.4 + - - +
401B GLU 3.9 15.9 - - - +
402B PHE* 4.1 19.1 - - + -
404B GLU* 4.3 23.8 - - + +
405B PHE* 4.0 40.2 - - + +
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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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85B TRP* 4.9 9.9 - - - -
141B GLU* 2.9 41.5 + - - +
142B HIS* 3.6 12.7 - - - +
144B LEU* 1.3 74.8 - - - +
146B GLU* 1.3 60.3 + - - +
148B ARG* 4.5 4.7 - - - +
149B ILE* 2.8 47.7 + - + +
243B ALA 3.4 24.4 + - - +
244B LYS* 4.0 20.2 - - - +
245B ARG 5.7 0.7 - - - -
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Residues in contact with GLU 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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127B LYS* 2.8 32.0 + - - +
129B LEU* 4.5 4.2 - - - +
142B HIS 2.9 17.2 + - - +
143B THR* 3.5 14.2 + - - +
145B ASN* 1.3 75.2 - - - +
147B LYS* 1.3 63.4 + - - +
149B ILE* 5.1 0.7 - - - -
150B LEU* 3.0 32.6 + - + +
173B MET* 3.5 29.5 - - - +
239B ASP* 4.5 1.0 - - - -
240B PHE* 3.3 37.8 + - + +
241B GLY* 3.4 21.0 + - - -
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Residues in contact with LYS 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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88B PRO* 4.3 6.1 - - - +
89B ALA 2.9 25.2 + - - -
90B GLN* 3.8 6.7 - - - +
143B THR 3.3 7.1 + - - +
144B LEU* 4.0 3.1 - - - +
146B GLU* 1.3 78.8 - - - +
148B ARG* 1.3 67.5 + - + +
151B GLN* 3.2 43.1 + - - +
161B LEU* 3.9 14.1 - - + +
164B SER* 3.3 25.3 + - - +
173B MET* 4.0 11.9 - - + -
404B GLU 4.0 4.9 + - - -
405B PHE* 2.8 66.6 + - + +
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Residues in contact with ARG 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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84B LYS 5.0 0.5 - - - +
85B TRP* 2.9 78.7 + - + +
86B GLU* 4.2 9.9 + - - +
88B PRO* 3.7 24.7 - - + +
144B LEU 3.1 20.5 + - - +
145B ASN* 4.0 2.7 - - - +
147B LYS* 1.3 85.2 - - + +
149B ILE* 1.3 61.9 + - - +
151B GLN* 3.7 9.3 - - - +
152B ALA* 3.4 21.7 + - - +
404B GLU* 5.3 8.4 + - - -
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Residues in contact with ILE 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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81B PHE* 4.7 1.8 - - + -
85B TRP* 3.5 26.7 - - + -
145B ASN* 2.8 24.5 + - + +
146B GLU 4.3 1.1 - - - +
148B ARG* 1.3 76.1 - - - +
150B LEU* 1.3 61.4 + - - +
152B ALA* 2.8 19.2 + - - +
153B VAL* 3.1 14.0 + - + +
217B LEU* 4.0 29.4 - - + -
240B PHE* 3.7 25.8 - - + -
243B ALA* 3.5 35.4 - - + +
244B LYS* 3.8 11.7 - - - +
245B ARG 4.0 8.1 - - - +
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Residues in contact with LEU 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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146B GLU* 3.0 22.1 + - + +
147B LYS* 4.3 1.6 - - - +
149B ILE* 1.3 78.1 - - - +
151B GLN* 1.3 62.5 + - - +
152B ALA 3.3 0.7 + - - -
153B VAL* 3.4 28.2 + - + +
158B LEU* 5.3 0.9 - - + -
159B VAL* 3.5 38.5 - - + +
160B LYS* 5.8 0.2 - - - -
161B LEU* 3.9 31.6 + - + +
173B MET* 5.6 6.1 - - - -
175B MET* 4.5 14.8 - - + -
239B ASP 5.6 1.6 - - - +
240B PHE* 3.9 42.8 - - + +
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Residues in contact with GLN 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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84B LYS* 3.8 16.9 + - + +
88B PRO* 3.3 17.6 - - - +
89B ALA* 2.9 55.8 + - - +
147B LYS* 3.2 34.2 + - - +
148B ARG* 3.7 6.8 - - - +
150B LEU* 1.3 78.1 - - - +
152B ALA* 1.3 61.4 + - + +
153B VAL 3.5 2.7 - - - +
161B LEU* 3.8 27.9 - - + +
163B PHE 6.0 0.3 - - - -
164B SER* 4.3 5.0 + - - -
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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