Contacts of the helix formed by residues 96 - 103 (chain A) in PDB entry 2MF9
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 ILE 96 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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70A LEU* 5.4 6.5 - - + -
95A VAL* 1.3 82.6 - - + +
97A GLN* 1.3 59.9 - - - +
98A ALA* 4.3 0.9 - - + -
99A LEU* 2.8 43.0 + - + +
100A ASP 2.9 9.9 + - - -
120A TYR 3.1 17.0 - - - +
121A CYS* 3.1 33.2 - - + +
122A TYR* 3.5 34.1 - - + +
140A LEU* 3.7 30.3 - - + -
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Residues in contact with GLN 97 (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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62A LYS* 5.0 0.4 - - - +
93A CYS* 3.3 31.4 - - - +
95A VAL 3.8 2.6 + - - -
96A ILE* 1.3 72.8 - - - +
98A ALA* 1.3 62.2 + - - +
100A ASP* 3.2 32.4 + - - +
101A LEU* 3.0 49.2 + - + +
120A TYR* 3.4 22.2 + - + +
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Residues in contact with ALA 98 (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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39A ILE* 4.0 4.9 - - - +
45A LEU* 3.6 19.4 - - + +
96A ILE* 4.3 8.1 - - + -
97A GLN* 1.3 77.6 - - - +
99A LEU* 1.3 56.4 + - - +
101A LEU* 3.9 2.3 - - - +
102A SER* 2.9 29.5 + - - -
114A VAL* 5.2 2.2 - - + -
116A ALA* 3.4 33.0 - - + -
120A TYR* 3.2 21.3 + - + +
140A LEU* 5.1 3.8 - - + -
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Residues in contact with LEU 99 (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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68A VAL* 3.7 25.8 - - + -
70A LEU* 5.4 6.7 - - + -
86A LEU* 4.4 5.6 - - + -
88A PHE* 3.7 17.9 - - + -
95A VAL* 4.0 14.8 - - + -
96A ILE* 2.8 23.9 + - + +
98A ALA* 1.3 75.6 - - - +
100A ASP* 1.3 66.2 + - - +
101A LEU 3.0 2.5 - - - -
102A SER* 4.0 5.6 - - - -
103A VAL* 3.0 43.3 + - + +
140A LEU* 4.7 5.8 - - + -
142A VAL* 3.5 40.4 - - + -
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Residues in contact with ASP 100 (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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62A LYS* 2.7 34.0 + - - -
88A PHE* 4.4 0.2 - - - -
89A THR 4.0 2.8 - - - +
90A LEU* 3.2 12.4 - - - +
91A GLY* 2.6 26.4 + - - -
93A CYS* 3.1 18.9 + - - -
94A ASP 4.2 1.0 + - - -
95A VAL* 3.8 12.5 - - + +
96A ILE 2.9 11.3 + - - +
97A GLN* 3.2 33.2 + - - +
99A LEU* 1.3 76.5 - - - +
101A LEU* 1.3 57.5 + - - +
104A PRO* 3.0 21.3 - - - +
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Residues in contact with LEU 101 (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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39A ILE* 3.8 20.4 - - + -
40A LEU* 4.0 28.9 - - + -
45A LEU* 4.2 10.1 - - + -
62A LYS* 3.3 28.5 - - - +
97A GLN* 3.0 31.4 + - + +
98A ALA 4.0 2.5 - - - +
99A LEU 3.0 0.2 - - - -
100A ASP* 1.3 78.7 - - - +
102A SER* 1.3 63.7 + - - +
103A VAL 3.2 2.7 - - - -
104A PRO* 3.1 13.1 - - + +
105A LEU* 3.2 23.4 - - + +
120A TYR* 5.8 0.4 - - + -
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Residues in contact with SER 102 (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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39A ILE* 3.9 14.1 - - - -
47A LYS* 3.3 10.6 - - - +
98A ALA 2.9 20.2 + - - -
99A LEU* 3.0 12.3 + - - -
101A LEU* 1.3 77.8 - - - +
103A VAL* 1.3 57.3 + - - +
105A LEU* 3.2 7.0 + - - +
106A MET* 2.8 38.1 + - - +
114A VAL* 3.2 30.3 - - - +
142A VAL* 4.3 0.2 - - - +
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Residues in contact with VAL 103 (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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60A PRO* 3.6 26.3 - - + +
66A VAL* 3.9 11.4 - - + -
68A VAL* 4.0 10.5 - - + -
88A PHE* 3.5 22.0 - - + -
90A LEU* 3.5 16.4 - - + -
99A LEU* 3.0 27.8 + - + +
102A SER* 1.3 72.0 - - - +
104A PRO* 1.4 62.7 - - + +
105A LEU 3.0 0.9 - - - -
106A MET* 2.7 43.4 + - + +
144A LEU* 4.0 7.7 - - + +
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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