Contacts of the helix formed by residues 151 - 159 (chain Q) in PDB entry 1MVW
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 LYS 151 (chain Q).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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98Q MET* 4.5 27.5 - - + +
101Q PHE* 5.2 0.8 - - - -
102Q LYS* 5.4 8.4 - - - +
109Q LYS* 4.6 22.0 + - - +
150Q TYR* 1.3 122.5 - - + +
152Q ASN* 1.3 67.1 + - - +
153Q ILE* 3.1 6.1 - - - +
154Q CYS* 3.3 20.1 + - - +
155Q TYR* 3.2 34.2 + - + -
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Residues in contact with ASN 152 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143Q ASP* 6.1 0.4 - - - +
144Q VAL* 4.4 16.7 - - + +
149Q ASP* 3.3 30.8 + - - +
150Q TYR 3.3 1.9 - - - +
151Q LYS* 1.3 80.4 - - - +
153Q ILE* 1.3 58.7 + - - +
155Q TYR* 3.4 13.7 + - - +
156Q VAL* 3.1 36.9 + - + +
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Residues in contact with ILE 153 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101Q PHE* 5.0 19.1 - - + -
117Q LEU* 6.5 0.4 - - + -
140Q PHE* 4.0 20.9 - - + -
144Q VAL* 2.0 75.6 - - + +
147Q ASN* 5.9 0.4 - - - -
149Q ASP 5.0 6.3 - - - +
150Q TYR* 5.5 2.5 - - + -
151Q LYS 3.1 4.7 - - - +
152Q ASN* 1.3 76.7 - - - +
154Q CYS* 1.3 57.7 + - - +
156Q VAL* 3.3 2.4 + - - +
157Q ILE* 2.9 53.0 + - + +
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Residues in contact with CYS 154 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94Q GLU* 3.4 11.4 - - + +
97Q ILE* 3.5 41.7 - - + +
98Q MET* 3.6 27.4 - - + -
101Q PHE* 3.6 21.1 - - - -
150Q TYR* 5.6 0.2 - - - -
151Q LYS* 3.3 19.0 + - - +
152Q ASN 3.3 0.4 - - - -
153Q ILE* 1.3 76.0 - - - +
155Q TYR* 1.3 67.7 + - + +
157Q ILE* 3.5 1.7 + - - +
158Q THR* 3.2 25.3 + - - -
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Residues in contact with TYR 155 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94Q GLU* 3.2 27.1 - - + -
98Q MET* 5.2 11.0 - - - -
151Q LYS* 3.2 19.7 + - + -
152Q ASN* 3.4 18.4 - - - +
153Q ILE 3.2 0.2 - - - -
154Q CYS* 1.3 79.4 - - + +
156Q VAL* 1.3 61.1 + - + +
158Q THR* 3.0 5.5 + - - -
159Q HIS* 2.8 53.0 + + + +
163Q ALA* 5.7 7.4 - - + -
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Residues in contact with VAL 156 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
823P PHE* 3.1 21.8 - - + -
140Q PHE* 3.6 28.7 - - + -
152Q ASN* 3.1 18.3 + - + +
155Q TYR* 1.3 78.6 - - + +
157Q ILE* 1.3 61.0 + - - +
159Q HIS* 3.0 9.5 - - - +
160Q GLY* 3.3 10.5 + - - -
161Q GLU 3.7 36.6 - - - +
162Q ASP* 5.4 1.3 - - - -
163Q ALA* 5.1 11.0 - - + +
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Residues in contact with ILE 157 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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819P ASN* 4.2 24.5 - - + +
820P VAL* 4.9 18.2 - - + -
823P PHE* 4.0 23.8 - - + +
832P MET* 5.8 1.2 - - - +
836P PHE* 5.0 2.4 - - - -
91Q ALA* 6.0 2.1 - - - +
92Q ASP 4.4 7.1 + - - +
97Q ILE* 3.9 30.5 - - + -
101Q PHE* 5.8 1.3 - - + -
140Q PHE* 3.9 17.7 - - + -
153Q ILE* 2.9 37.6 + - + +
154Q CYS 3.9 4.0 - - - +
155Q TYR 3.3 0.2 - - - -
156Q VAL* 1.3 78.1 - - - +
158Q THR* 1.3 60.8 + - - +
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Residues in contact with THR 158 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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832P MET* 4.1 9.7 - - - +
835P PHE* 4.6 0.7 - - - -
836P PHE* 3.2 10.9 - - - -
839P MLY 3.1 44.8 + - - -
92Q ASP 3.3 19.9 + - - +
93Q PRO* 4.9 6.1 - - + -
94Q GLU* 3.2 34.5 + - + +
97Q ILE* 4.0 0.3 - - - +
154Q CYS 3.2 5.0 + - - -
155Q TYR 3.0 3.4 + - - -
157Q ILE* 1.3 77.8 - - - +
159Q HIS* 1.3 61.1 + - - +
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Residues in contact with HIS 159 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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836P PHE* 2.4 30.7 - - + +
839P MLY 3.1 49.8 - - + -
94Q GLU* 3.3 17.3 + - - -
155Q TYR* 2.8 45.5 + + + +
156Q VAL* 3.0 17.7 - - + +
158Q THR* 1.3 69.0 - - - +
160Q GLY* 1.3 66.2 + - - +
161Q GLU 4.2 0.9 + - - +
163Q ALA* 5.2 12.5 - - + +
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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