Contacts of the helix formed by residues 139 - 151 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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109A PHE* 3.5 40.7 - - + -
134A VAL* 2.9 21.9 + - + +
137A LEU* 3.1 26.3 + - + +
138A LYS* 1.3 85.0 + - - +
140A ILE* 1.3 63.9 + - - +
141A GLU 3.5 2.2 - - - -
142A HIS* 2.8 39.6 + - + +
143A THR* 2.7 35.0 + - - +
242A PHE* 3.7 12.5 - - - -
22I ILE 5.4 0.4 + - - -
23I HIS* 4.8 7.5 + - - +
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Residues in contact with ILE 140 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134A VAL* 3.7 6.3 - - - +
135A VAL* 3.8 45.1 - - + +
138A LYS* 3.6 3.7 - - - -
139A GLN* 1.3 77.3 - - - +
141A GLU* 1.3 65.3 + - - +
143A THR* 3.8 1.2 - - - -
144A LEU* 3.0 33.1 + - + +
401A GLU* 3.8 39.3 - - + +
402A PHE* 4.1 13.6 - - + -
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Residues in contact with GLU 141 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138A LYS 5.4 0.8 + - - -
140A ILE* 1.3 80.1 - - - +
142A HIS* 1.3 64.0 + - + +
144A LEU* 3.4 9.7 + - + +
145A ASN* 2.9 48.8 + - - +
244A LYS* 4.1 23.6 + - - +
252A TPO 4.5 6.7 + - - -
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Residues in contact with HIS 142 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138A LYS 4.7 4.4 + - - -
139A GLN* 2.8 43.1 + - + +
140A ILE 3.2 0.6 - - - -
141A GLU* 1.3 84.7 - - + +
143A THR* 1.3 56.9 + - - +
145A ASN* 3.3 15.2 + - - +
146A GLU* 2.9 28.6 + - - +
220A ARG* 3.9 9.6 + - - -
241A GLY* 3.3 21.8 - - - +
242A PHE* 3.8 17.0 - + - -
252A TPO 2.8 49.7 + - + +
254A CYS* 4.4 6.7 - - + -
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Residues in contact with THR 143 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129A LEU* 3.6 23.9 - - + +
134A VAL* 3.5 18.6 - - + +
139A GLN* 2.7 26.3 + - - +
140A ILE 3.8 2.9 - - - -
142A HIS* 1.3 75.6 - - - +
144A LEU* 1.3 65.4 + - - +
146A GLU* 3.3 12.2 + - - +
147A LYS* 3.2 23.0 + - - +
171A LEU* 3.6 30.1 - - + -
173A MET* 4.7 1.1 - - + -
402A PHE* 4.7 2.0 - - + -
405A PHE* 4.4 8.4 - - + -
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Residues in contact with LEU 144 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140A ILE* 3.0 31.4 + - + +
141A GLU* 3.7 7.6 - - + +
143A THR* 1.3 76.4 - - - +
145A ASN* 1.3 62.2 + - - +
147A LYS* 3.5 2.6 + - - +
148A ARG* 3.0 26.1 + - - +
401A GLU 3.9 15.0 - - - +
402A PHE* 4.2 17.9 - - + -
404A GLU* 3.6 45.4 - - + +
405A PHE* 4.0 28.7 - - + +
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Residues in contact with ASN 145 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85A TRP* 4.9 10.1 - - - -
141A GLU* 2.9 43.9 + - - +
142A HIS* 3.4 18.3 - - - +
144A LEU* 1.3 71.1 - - - +
146A GLU* 1.3 59.0 + - - +
148A ARG* 4.6 4.3 - - - +
149A ILE* 2.7 48.4 + - + +
243A ALA 3.4 24.5 + - - +
244A LYS* 4.0 19.9 - - - +
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Residues in contact with GLU 146 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127A LYS* 2.8 32.3 + - - +
129A LEU* 4.3 5.5 - - - +
142A HIS 2.9 15.0 + - - +
143A THR* 3.3 14.5 + - - +
145A ASN* 1.3 74.1 - - - +
147A LYS* 1.3 59.5 + - - +
149A ILE* 5.1 0.4 - - - -
150A LEU* 2.9 38.4 + - + +
173A MET* 3.6 26.4 - - - +
239A ASP* 4.5 0.9 - - - -
240A PHE* 3.3 37.9 + - + +
241A GLY* 3.5 21.1 + - - -
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Residues in contact with LYS 147 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88A PRO* 4.2 6.7 - - - +
89A ALA 2.9 25.1 + - - -
90A GLN* 3.9 5.5 - - - +
143A THR 3.2 7.4 + - - +
144A LEU 4.1 2.9 - - - +
146A GLU* 1.3 79.5 - - - +
148A ARG* 1.3 67.9 + - + +
151A GLN* 3.1 42.9 + - - +
161A LEU* 3.9 16.1 - - + +
164A SER* 3.3 24.0 - - - +
173A MET* 4.0 11.2 - - - -
404A GLU 4.0 5.5 + - - -
405A PHE* 2.9 67.9 + - + +
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Residues in contact with ARG 148 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84A LYS 5.1 0.9 - - - +
85A TRP* 2.9 79.9 + - + +
86A GLU* 4.3 7.9 + - - +
88A PRO* 3.8 24.3 - - + +
144A LEU 3.0 19.1 + - - +
145A ASN* 3.9 2.9 - - - +
147A LYS* 1.3 85.6 - - + +
149A ILE* 1.3 61.2 + - - +
151A GLN* 3.8 8.0 - - - +
152A ALA* 3.4 20.4 + - - +
404A GLU* 4.1 24.6 + - - +
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Residues in contact with ILE 149 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81A PHE* 4.7 1.1 - - + -
85A TRP* 3.5 26.0 - - + -
145A ASN* 2.7 30.3 + - + +
146A GLU 4.3 0.7 - - - +
148A ARG* 1.3 71.2 - - - +
150A LEU* 1.3 61.3 + - - +
152A ALA* 2.8 20.8 + - - +
153A VAL* 3.2 13.6 + - + +
217A LEU* 4.0 28.3 - - + -
240A PHE* 3.8 25.6 - - + -
243A ALA* 3.5 35.9 - - + +
244A LYS* 3.7 15.9 - - - +
245A ARG 4.0 4.0 - - - +
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Residues in contact with LEU 150 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146A GLU* 2.9 24.4 + - + +
147A LYS 4.3 0.9 - - - +
149A ILE* 1.3 77.9 - - - +
151A GLN* 1.3 62.6 + - - +
152A ALA 3.2 0.7 + - - -
153A VAL* 3.5 27.2 + - + +
158A LEU* 5.2 0.9 - - + -
159A VAL* 3.5 40.0 - - + +
161A LEU* 3.9 31.3 + - + +
173A MET* 5.7 3.6 - - - -
175A MET* 4.5 13.7 - - + -
239A ASP 5.6 2.0 - - - +
240A PHE* 3.8 43.9 - - + +
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Residues in contact with GLN 151 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84A LYS* 3.7 17.4 + - + +
88A PRO* 3.4 16.2 - - - +
89A ALA* 3.0 53.0 + - - +
147A LYS* 3.1 34.6 + - - +
148A ARG* 3.8 6.1 - - - +
150A LEU* 1.3 78.7 - - - +
152A ALA* 1.3 61.9 + - + +
153A VAL 3.6 3.0 - - - +
161A LEU* 3.9 27.9 - - + +
163A PHE 5.9 0.5 - - - -
164A SER* 4.3 5.9 + - - -
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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