Contacts of the helix formed by residues 93 - 105 (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 PRO 93 (chain Q).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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20Q ASP* 4.4 17.3 - - + +
23Q GLU* 5.8 5.4 - - - +
91Q ALA 4.1 4.7 - - - +
92Q ASP* 1.3 98.8 - - - +
94Q GLU* 1.3 64.4 + - - +
95Q ASP* 3.2 9.6 - - + +
96Q VAL* 3.0 29.6 + - + -
97Q ILE* 3.1 11.8 - - - +
158Q THR* 4.2 8.1 - - + +
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Residues in contact with GLU 94 (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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839P MLY 4.5 7.2 - - - -
93Q PRO* 1.3 71.8 - - - +
95Q ASP* 1.3 63.6 + - - +
97Q ILE* 3.2 10.1 + - - +
98Q MET* 2.9 42.2 + - - +
154Q CYS* 3.4 15.0 - - + +
155Q TYR* 3.2 40.9 - - + -
158Q THR* 3.2 28.3 + - + +
159Q HIS* 3.3 14.8 + - - -
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Residues in contact with ASP 95 (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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93Q PRO* 3.1 5.9 + - + +
94Q GLU* 1.3 82.7 + - - +
96Q VAL* 1.3 63.2 + - + +
98Q MET* 3.6 9.8 + - - +
99Q GLY* 3.0 22.7 + - - -
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Residues in contact with VAL 96 (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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815P CYS* 4.1 12.6 - - - -
92Q ASP* 3.1 27.1 - - - +
93Q PRO* 3.0 22.7 + - + +
95Q ASP* 1.3 80.4 - - + +
97Q ILE* 1.3 59.3 + - - +
99Q GLY* 3.3 2.6 + - - +
100Q ALA* 3.0 27.2 + - - +
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Residues in contact with ILE 97 (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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815P CYS* 6.2 0.2 - - - -
816P ILE* 5.8 5.2 - - + -
819P ASN* 5.9 0.4 - - + -
92Q ASP* 3.1 40.2 - - + +
93Q PRO 3.1 11.2 + - - +
94Q GLU* 3.2 4.7 + - - +
96Q VAL* 1.3 78.4 - - - +
98Q MET* 1.3 57.1 + - - +
100Q ALA* 3.3 6.2 + - - +
101Q PHE* 3.0 58.7 + - + -
154Q CYS* 3.5 30.7 - - + +
157Q ILE* 3.9 30.7 - - + -
158Q THR* 4.0 0.4 - - - +
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Residues in contact with MET 98 (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* 2.9 29.0 + - - +
95Q ASP* 4.0 8.7 - - - +
97Q ILE* 1.3 75.2 - - - +
99Q GLY* 1.3 57.1 + - - +
101Q PHE* 3.7 7.0 - - - -
102Q LYS* 2.9 31.8 + - - +
150Q TYR* 5.8 0.8 - - - -
151Q LYS* 4.5 31.4 - - + +
154Q CYS* 3.6 22.9 - - - -
155Q TYR* 5.2 11.7 - - - -
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Residues in contact with GLY 99 (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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95Q ASP 3.0 16.5 + - - -
96Q VAL* 3.3 5.3 + - - -
97Q ILE 3.3 0.4 - - - -
98Q MET* 1.3 74.3 - - - +
100Q ALA* 1.3 61.1 + - - +
102Q LYS* 3.1 17.1 + - - +
103Q VAL* 3.1 20.2 + - - +
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Residues in contact with ALA 100 (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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812P SER* 4.9 15.5 - - - +
815P CYS* 6.0 2.7 - - + -
816P ILE* 3.5 33.4 - - + -
96Q VAL 3.0 13.4 + - - +
97Q ILE* 3.6 7.6 - - - +
99Q GLY* 1.3 72.6 - - - +
101Q PHE* 1.3 57.5 + - - +
103Q VAL* 3.2 11.4 + - - +
104Q LEU* 3.0 31.7 + - - +
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Residues in contact with PHE 101 (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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816P ILE* 4.6 15.7 - - + -
97Q ILE* 3.0 42.4 + - + +
98Q MET* 3.9 5.4 - - - +
99Q GLY 3.3 0.2 - - - -
100Q ALA* 1.3 77.4 - - - +
102Q LYS* 1.3 57.1 + - - +
104Q LEU* 3.4 24.7 + - + +
105Q ASP 2.9 21.3 + - - -
117Q LEU* 5.2 13.9 - - + -
150Q TYR* 3.1 54.3 + + + -
151Q LYS 5.2 1.1 - - - -
153Q ILE* 5.0 21.5 - - + -
154Q CYS* 3.6 20.4 - - - -
157Q ILE* 5.8 1.3 - - + -
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Residues in contact with LYS 102 (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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98Q MET 2.9 17.8 + - - +
99Q GLY* 3.1 7.8 + - - +
101Q PHE* 1.3 74.7 - - - +
103Q VAL* 1.3 62.1 + - + +
105Q ASP* 3.0 30.6 - - - +
106Q PRO* 3.2 9.0 - - + +
108Q GLY* 3.6 27.8 - - - +
109Q LYS* 3.7 11.7 - - - +
150Q TYR* 5.6 4.7 - - + +
151Q LYS* 5.4 9.0 - - - +
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Residues in contact with VAL 103 (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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812P SER* 5.9 6.5 - - - +
99Q GLY 3.1 17.5 + - - +
100Q ALA* 3.2 11.6 + - - +
102Q LYS* 1.3 80.9 - - + +
104Q LEU* 1.3 64.5 + - + +
106Q PRO* 3.7 17.5 - - - +
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Residues in contact with LEU 104 (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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816P ILE* 4.8 10.1 - - + -
100Q ALA 3.0 12.7 + - - +
101Q PHE* 3.7 37.7 - - + +
102Q LYS 3.3 0.2 - - - -
103Q VAL* 1.3 83.9 - - + +
105Q ASP* 1.3 57.7 + - - +
106Q PRO* 3.3 8.2 - - - +
112Q ILE* 3.3 30.6 - - + +
116Q PHE* 5.0 5.0 - - + -
117Q LEU* 4.2 15.5 - - + -
120Q LEU* 3.7 28.9 - - + -
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Residues in contact with ASP 105 (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 2.9 5.6 + - - +
102Q LYS* 3.0 13.7 - - - +
104Q LEU* 1.3 78.0 - - - +
106Q PRO* 1.3 58.5 - - - +
107Q ASP* 3.1 13.5 - - - +
108Q GLY* 3.0 37.6 + - - +
109Q LYS 3.8 0.7 + - - -
110Q GLY* 2.9 28.8 - - - +
111Q SER 4.9 0.3 - - - -
112Q ILE* 4.8 10.2 + - + +
150Q TYR* 2.9 25.6 + - + +
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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