Contacts of the helix formed by residues 88 - 94 (chain M) in PDB entry 2I2X
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 VAL 88 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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46M ALA* 6.3 0.7 - - + -
47M PRO* 4.0 25.6 - - + -
58M LEU* 4.1 10.8 - - + -
62M TYR* 4.4 3.8 - - - +
86M GLU 3.3 3.4 + - - +
87M HIS* 1.3 80.4 - - - +
89M GLN* 1.3 67.3 + - - +
90M GLN* 3.3 32.1 - - + +
91M MET* 2.9 40.7 + - + +
184N MET* 6.3 2.7 - - + -
186N THR* 6.5 0.2 - - + -
500N B13 5.8 3.6 - - - -
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Residues in contact with GLN 89 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87M HIS 4.0 0.4 + - - -
88M VAL* 1.3 70.7 - - + +
90M GLN* 1.3 101.1 + - - +
92M SER* 3.0 7.5 + - - +
93M ASN* 2.8 56.0 + - - +
127M GLY* 6.2 1.8 - - - -
129M ILE* 4.4 8.5 - - + +
500N B13 5.6 7.2 - - + +
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Residues in contact with GLN 90 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52M GLY* 3.5 36.0 + - - -
58M LEU* 4.3 4.5 - - + +
88M VAL* 3.3 28.2 - - + +
89M GLN* 1.3 115.1 + - - +
91M MET* 1.3 56.7 - - - +
93M ASN* 4.5 1.3 - - - +
94M ASN* 3.1 43.7 + - - +
97M TRP* 3.7 32.2 - - + +
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Residues in contact with MET 91 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58M LEU* 3.8 18.8 - - + -
62M TYR* 3.7 33.2 - - + -
85M THR* 3.8 21.3 - - + -
87M HIS* 3.6 28.6 + - + +
88M VAL* 2.9 37.3 + - + +
90M GLN* 1.3 76.5 - - - +
92M SER* 1.3 57.5 + - - +
94M ASN 3.3 15.0 - - - +
95M PRO* 3.9 4.5 - - - +
97M TRP* 4.0 4.3 - - + -
98M GLY* 3.4 28.2 + - - +
101M VAL* 3.9 20.0 - - + -
124M HIS* 4.4 1.3 - - - +
149M ALA* 5.1 0.5 - - - +
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Residues in contact with SER 92 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87M HIS* 2.7 28.5 + - - +
88M VAL 3.8 0.2 + - - -
89M GLN* 3.0 8.3 + - - -
91M MET* 1.3 77.3 - - - +
93M ASN* 1.3 64.5 + - - +
94M ASN 3.2 1.2 + - - -
95M PRO* 3.6 13.5 - - - +
126M ILE* 3.7 6.9 - - - +
127M GLY* 2.9 25.9 + - - -
129M ILE* 3.8 25.8 - - - +
145M VAL* 3.8 9.0 - - - +
149M ALA* 4.1 10.8 - - - +
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Residues in contact with ASN 93 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89M GLN* 2.8 50.0 + - - +
92M SER* 1.3 72.5 - - - +
94M ASN* 1.3 67.4 + - - +
95M PRO* 3.2 9.1 - - - +
129M ILE* 3.6 34.3 - - - +
142M LYS* 4.4 12.0 - - - +
145M VAL* 3.7 9.7 - - - +
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Residues in contact with ASN 94 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90M GLN* 3.1 34.2 + - - +
91M MET 3.3 6.2 - - - +
93M ASN* 1.3 84.1 - - - +
95M PRO* 1.3 67.1 - - - +
96M SER* 3.2 3.6 - - - +
97M TRP* 2.8 54.5 + - + +
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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