Contacts of the helix formed by residues 154 - 169 (chain B) in PDB entry 4MHV
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 PHE 154 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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152B PRO 3.4 1.6 + - - -
153B ASP* 1.3 89.7 - - + +
155B VAL* 1.4 62.2 + - + +
156B GLY 3.3 1.3 - - - -
157B ASP* 3.2 36.6 + - - +
158B ILE* 3.6 10.1 + - - +
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Residues in contact with VAL 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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124B LEU* 3.8 43.5 - - + -
126B ASN* 4.4 9.4 - - + +
127B VAL* 5.5 2.0 - - + -
152B PRO* 4.1 27.4 - - + -
153B ASP 3.0 12.1 + - - +
154B PHE* 1.4 71.8 - - + +
156B GLY* 1.3 59.7 + - - +
158B ILE* 2.9 30.9 + - + +
159B LEU* 3.1 23.6 + - + +
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Residues in contact with GLY 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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147B PHE* 3.4 5.6 - - - -
148B LEU* 3.4 13.5 - - - -
151B ALA* 3.5 28.7 - - - +
152B PRO 3.0 13.9 + - - -
155B VAL* 1.3 77.0 - - - +
157B ASP* 1.3 50.9 + - - +
159B LEU* 3.4 2.0 + - - -
160B TRP* 2.8 36.6 + - - +
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Residues in contact with ASP 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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144B LYS* 5.8 4.5 + - - +
148B LEU* 3.8 21.1 - - - +
154B PHE* 3.3 32.8 + - - +
155B VAL 3.2 0.2 - - - -
156B GLY* 1.3 72.8 + - - +
158B ILE* 1.4 62.7 + - + +
160B TRP* 3.9 4.1 - - - +
161B GLU* 3.2 23.9 + - - +
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Residues in contact with ILE 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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83B LEU* 3.7 34.3 - - + -
87B PHE* 3.5 16.2 - - + -
122B PHE* 4.1 29.6 - - + -
124B LEU* 4.9 13.2 - - + -
154B PHE 3.6 10.1 + - - +
155B VAL* 2.9 18.1 + - + +
157B ASP* 1.4 76.3 - - + +
159B LEU* 1.3 67.4 + - + +
161B GLU* 3.3 14.7 + - - +
162B HIS* 3.3 8.7 + - - +
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Residues in contact with LEU 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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114B TRP* 3.4 24.1 - - + +
115B LEU* 3.8 24.2 - - + -
118B ALA* 3.6 31.2 - - + -
122B PHE* 5.5 1.1 - - + -
124B LEU* 4.4 7.9 - - + -
127B VAL* 4.7 10.1 - - + +
132B PHE* 5.5 0.9 - - + -
147B PHE* 3.6 22.9 - - + -
151B ALA* 4.6 9.9 - - + -
152B PRO* 5.2 1.3 - - + -
155B VAL* 3.1 33.0 + - + +
156B GLY 3.9 2.0 - - - +
158B ILE* 1.3 79.3 - - + +
160B TRP* 1.3 58.4 + - - +
162B HIS* 3.3 6.2 + - + +
163B LEU* 2.9 25.6 + - - +
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Residues in contact with TRP 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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139B LEU 5.4 1.8 - - - -
140B CYS 6.0 1.3 - - - -
142B LEU* 5.6 0.2 - - + -
143B GLY* 3.6 22.9 - - - -
144B LYS* 3.4 58.9 - - + +
147B PHE* 3.5 30.7 - + + -
148B LEU* 4.5 4.0 - - + -
156B GLY 2.8 23.5 + - - +
157B ASP* 3.9 5.8 - - - +
159B LEU* 1.3 73.2 - - - +
161B GLU* 1.4 56.0 + - - +
163B LEU* 3.8 24.7 - - + -
164B GLU* 2.8 75.6 + - + +
167B ILE* 5.5 6.5 - - + -
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Residues in contact with GLU 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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80B SER* 4.3 18.8 + - - +
83B LEU* 5.7 3.1 - - - +
84B LYS* 3.4 47.0 + - - +
87B PHE* 3.9 16.6 - - + -
157B ASP 3.2 12.0 + - - +
158B ILE* 3.3 11.7 + - - +
160B TRP* 1.4 79.0 - - - +
162B HIS* 1.3 56.9 + - - +
164B GLU* 3.8 14.8 - - - +
165B GLN* 3.1 29.3 + - - +
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Residues in contact with HIS 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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87B PHE* 3.5 54.3 + + + -
90B PHE* 3.5 37.1 - + + -
114B TRP* 3.1 22.9 + - - +
117B TRP* 3.6 17.1 - + - -
118B ALA* 5.9 0.2 - - - +
122B PHE* 5.9 0.2 - - - -
158B ILE 3.3 3.9 + - - +
159B LEU* 3.3 11.7 + - + +
160B TRP 3.2 0.6 - - - -
161B GLU* 1.3 76.7 - - - +
163B LEU* 1.3 66.0 + - - +
165B GLN* 3.2 7.7 + - - +
166B MET* 3.0 45.4 + - + +
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Residues in contact with LEU 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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103B PRO* 4.3 13.2 - - + -
106B TRP* 5.1 3.8 - - + -
114B TRP* 3.9 14.3 - - + -
139B LEU* 3.7 48.7 - - + +
140B CYS* 5.2 0.7 - - - -
147B PHE* 4.0 14.6 - - + -
159B LEU 2.9 19.7 + - - +
160B TRP* 3.8 30.1 - - + +
162B HIS* 1.3 72.5 - - - +
164B GLU* 1.3 62.4 + - - +
166B MET* 3.2 9.2 + - + +
167B ILE* 3.0 49.3 + - + +
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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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84B LYS* 5.5 2.8 + - - -
160B TRP* 2.8 58.3 + - + +
161B GLU* 3.8 13.5 - - - +
163B LEU* 1.3 70.8 - - - +
165B GLN* 1.4 56.8 + - - +
167B ILE* 3.2 10.7 + - - +
168B LYS* 2.9 32.0 + - + +
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Residues in contact with GLN 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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84B LYS* 3.7 30.5 + - - +
87B PHE* 3.8 31.7 - - - +
91B LYS* 5.3 9.0 - - - +
161B GLU 3.1 19.2 + - - +
162B HIS* 3.6 7.8 - - - +
164B GLU* 1.4 75.0 + - - +
166B MET* 1.3 58.1 + - - +
168B LYS* 3.3 11.1 + - - +
169B GLU* 2.9 65.6 + - - +
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Residues in contact with MET 166 (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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90B PHE* 3.3 32.1 - - + -
94B GLN* 3.4 21.5 - - - +
101B LYS 4.2 6.3 - - - +
103B PRO* 3.7 19.6 - - + +
106B TRP* 3.6 18.6 - - + -
114B TRP* 4.5 3.6 - - - -
162B HIS* 3.0 53.1 + - + +
163B LEU* 3.4 11.0 - - - +
165B GLN* 1.3 78.3 - - + +
167B ILE* 1.3 52.4 + - - +
169B GLU 2.6 21.5 - - - +
170B ASN* 3.4 20.2 - - - +
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Residues in contact with ILE 167 (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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102B ASN* 5.5 3.5 - - - +
103B PRO* 4.2 8.7 - - + -
140B CYS* 4.0 43.1 - - + +
160B TRP* 5.5 6.3 - - + -
163B LEU* 3.0 47.1 + - + +
164B GLU* 3.7 7.4 - - - +
166B MET* 1.3 74.1 - - - +
168B LYS* 1.4 66.6 + - - +
169B GLU 3.6 3.5 - - - +
170B ASN 4.6 3.9 - - - +
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Residues in contact with LYS 168 (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* 5.8 4.2 - - - +
164B GLU* 2.9 19.5 + - + +
165B GLN* 3.3 9.5 + - - +
167B ILE* 1.4 80.1 - - - +
169B GLU* 1.3 81.0 + - - +
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Residues in contact with GLU 169 (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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91B LYS* 5.0 8.0 + - - -
165B GLN* 2.9 43.4 + - - +
166B MET 2.6 22.3 - - - +
167B ILE 3.6 2.0 - - - +
168B LYS* 1.3 99.5 + - - +
170B ASN* 1.3 77.0 + - - +
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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