Contacts of the helix formed by residues 102 - 114 (chain F) in PDB entry 3H2V
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 ASN 102 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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59F ARG* 3.3 23.2 - - - +
100F LEU* 3.3 1.2 - - - +
101F LEU* 1.3 98.2 - - - +
103F GLY* 1.3 63.5 + - - +
104F GLU* 3.0 30.3 + - - +
105F GLN* 3.0 19.4 + - - +
106F ALA 3.2 17.8 + - - -
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Residues in contact with GLY 103 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58F MET* 3.4 22.6 - - - +
59F ARG* 4.0 2.8 - - - +
102F ASN* 1.3 77.0 - - - +
104F GLU* 1.3 63.5 + - - +
106F ALA* 3.6 2.4 + - - +
107F GLU* 3.2 22.9 + - - +
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Residues in contact with GLU 104 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102F ASN* 3.0 11.3 + - - +
103F GLY* 1.3 78.4 - - - +
105F GLN* 1.3 63.5 + - + +
107F GLU* 3.1 18.4 + - - +
108F ALA* 3.1 23.9 + - + +
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Residues in contact with GLN 105 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81F ASP 4.3 2.8 + - - -
82F TYR* 3.6 31.3 - - + +
83F GLU* 3.3 25.2 + - - +
100F LEU* 3.7 14.3 - - + +
101F LEU* 3.1 39.0 + - + +
102F ASN* 3.0 26.7 + - - +
104F GLU* 1.3 76.5 - - + +
106F ALA* 1.3 57.5 + - - +
107F GLU 3.1 0.2 + - - -
108F ALA* 3.3 4.2 + - - +
109F ALA* 2.8 30.8 + - - +
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Residues in contact with ALA 106 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58F MET 3.9 7.9 - - - +
59F ARG* 3.7 39.0 - - - +
61F ILE* 3.8 14.6 - - + +
100F LEU* 3.8 11.8 - - + +
102F ASN 3.2 4.8 + - - +
103F GLY 3.9 1.6 - - - +
105F GLN* 1.3 78.7 - - - +
107F GLU* 1.3 56.5 + - - +
109F ALA* 3.8 0.4 - - - +
110F ILE* 3.0 36.4 + - - +
127F LEU* 4.4 7.0 - - + -
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Residues in contact with GLU 107 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103F GLY 3.2 13.9 + - - +
104F GLU* 3.1 25.1 + - - +
106F ALA* 1.3 74.4 - - - +
108F ALA* 1.3 62.2 + - - +
110F ILE* 3.2 11.8 + - - +
111F ASN* 2.9 51.4 + - - +
127F LEU* 6.0 0.4 - - - -
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Residues in contact with ALA 108 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82F TYR* 3.5 20.4 - - + +
104F GLU* 3.1 11.3 + - + +
105F GLN* 3.8 3.6 - - - +
107F GLU* 1.3 76.7 - - - +
109F ALA* 1.3 59.6 + - - +
111F ASN* 4.1 4.8 - - - +
112F ALA* 2.8 34.1 + - - +
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Residues in contact with ALA 109 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61F ILE* 4.8 13.2 - - + -
79F LEU* 5.3 3.8 - - + -
82F TYR* 3.7 19.7 + - + -
100F LEU* 3.7 21.5 - - + -
105F GLN 2.8 17.9 + - - +
106F ALA* 3.8 4.3 - - - +
108F ALA* 1.3 77.8 - - - +
110F ILE* 1.3 63.2 + - - +
113F PHE* 3.0 35.3 + - + +
125F VAL* 4.2 3.7 - - + +
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Residues in contact with ILE 110 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61F ILE* 3.6 13.5 - - + -
106F ALA 3.0 27.5 + - - +
107F GLU* 3.5 12.3 - - - +
109F ALA* 1.3 75.0 - - - +
111F ASN* 1.3 63.3 + - - +
114F HIS* 2.7 42.6 + - + +
125F VAL* 3.7 22.9 - - + +
126F GLN* 4.1 8.7 - - - -
127F LEU* 3.3 46.9 - - + +
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Residues in contact with ASN 111 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107F GLU* 2.9 43.6 + - - +
108F ALA* 4.1 5.5 - - - +
110F ILE* 1.3 82.6 - - - +
112F ALA* 1.3 66.4 + - - +
113F PHE 3.4 0.3 + - - -
114F HIS* 4.1 8.1 + - - +
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Residues in contact with ALA 112 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82F TYR* 4.2 7.0 - - - +
108F ALA 2.8 21.5 + - - +
111F ASN* 1.3 74.4 - - - +
113F PHE* 1.3 85.8 + - + +
114F HIS 5.0 1.0 - - - +
116F SER* 4.3 8.3 - - - -
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Residues in contact with PHE 113 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78F LEU* 3.2 44.9 - - + -
79F LEU* 3.8 21.8 - - + -
81F ASP* 6.2 2.0 - - + -
82F TYR* 3.8 23.6 - + - -
109F ALA* 3.0 25.3 + - - +
112F ALA* 1.3 94.5 - - + +
114F HIS* 1.3 57.8 + - - +
115F GLN 3.5 2.3 + - - -
116F SER* 3.3 27.9 + - - +
123F LEU* 3.9 5.4 - - + +
125F VAL* 2.7 31.8 - - + +
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Residues in contact with HIS 114 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110F ILE* 2.7 29.0 + - + +
111F ASN* 4.5 6.4 - - - +
112F ALA 3.8 1.6 - - - +
113F PHE* 1.3 71.1 - - - +
115F GLN* 1.3 94.3 + - + +
116F SER 3.7 0.3 + - - -
124F SER* 3.6 20.5 - - - -
125F VAL* 3.0 39.1 + - - +
126F GLN* 5.6 3.8 - - + -
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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