Contacts of the helix formed by residues 98 - 110 (chain U) in PDB entry 3A0B
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 THR 98 (chain U).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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96U GLY 4.5 3.1 - - - +
97U LEU* 1.3 71.9 - - - +
99U GLU* 1.3 64.2 + - - +
100U ARG* 2.5 18.3 + - - +
101U GLN* 2.4 62.2 + - - +
102U LYS* 2.8 5.7 + - - -
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Residues in contact with GLU 99 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97U LEU 3.7 5.1 + - - +
98U THR* 1.3 79.0 - - - +
100U ARG* 1.3 52.6 + - + +
102U LYS* 3.5 23.2 - - - +
103U GLN* 2.7 35.2 + - - +
106U ARG* 4.1 6.8 + - - +
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Residues in contact with ARG 100 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69U ARG* 5.2 14.5 - - - +
98U THR* 2.5 15.6 + - - +
99U GLU* 1.3 77.8 - - + +
101U GLN* 1.3 57.2 + - - +
103U GLN* 2.8 43.7 + - - +
104U ILE* 2.9 28.8 + - + +
107U GLU* 4.0 16.9 + - - -
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Residues in contact with GLN 101 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74U THR* 4.8 8.1 + - - -
75U LEU* 3.6 31.1 - - + +
78U LEU* 4.4 12.3 - - - +
96U GLY 3.5 5.2 - - - +
97U LEU* 3.5 15.2 - - + -
98U THR* 2.4 72.6 + - + +
100U ARG* 1.3 67.8 - - - +
102U LYS* 1.3 60.9 + - - +
103U GLN 2.9 2.3 + - - -
104U ILE* 3.9 14.1 - - + +
105U LEU* 2.8 33.5 + - - +
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Residues in contact with LYS 102 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92U LEU* 3.3 28.1 + - + +
93U ASN 5.2 1.3 - - - +
97U LEU* 3.2 34.7 - - + +
98U THR 2.8 10.7 + - - +
99U GLU* 3.6 23.1 - - - +
101U GLN* 1.3 76.5 - - - +
103U GLN* 1.3 63.5 + - - +
105U LEU* 3.3 10.8 - - - +
106U ARG* 3.3 40.4 + - - +
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Residues in contact with GLN 103 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99U GLU 2.7 13.6 + - - +
100U ARG* 2.8 31.4 + - - +
102U LYS* 1.3 73.0 - - - +
104U ILE* 1.3 59.2 + - - +
105U LEU 2.8 1.8 - - - -
106U ARG* 2.3 66.9 + - - +
107U GLU* 3.2 24.2 + - - +
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Residues in contact with ILE 104 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69U ARG* 3.9 14.8 - - - +
70U GLY* 3.6 27.8 - - - +
71U LEU* 4.2 3.8 - - + -
75U LEU* 4.2 10.3 - - + -
100U ARG* 2.9 37.1 + - + +
101U GLN* 3.9 15.7 - - + +
103U GLN* 1.3 74.0 - - - +
105U LEU* 1.3 62.6 + - - +
107U GLU* 3.3 15.9 + - + +
108U ASN* 2.9 45.5 + - - +
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Residues in contact with LEU 105 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71U LEU* 6.2 0.2 - - + -
75U LEU* 3.3 39.5 - - + -
79U ILE* 5.0 5.2 - - + -
91U VAL* 3.4 33.9 - - + -
92U LEU* 3.8 13.2 - - + -
94U ILE* 5.1 2.7 - - + -
97U LEU* 3.4 31.6 - - + -
101U GLN 2.8 17.6 + - - +
102U LYS* 3.3 7.9 - - - +
103U GLN 2.5 4.0 + - - -
104U ILE* 1.3 77.0 - - - +
106U ARG* 1.3 52.4 + - - +
108U ASN* 3.4 1.1 - - - -
109U LEU* 2.6 43.2 + - + +
112U PHE* 4.5 14.0 - - + -
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Residues in contact with ARG 106 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92U LEU* 3.3 36.3 - - + +
99U GLU* 4.1 9.5 + - - +
102U LYS* 3.3 28.8 + - - +
103U GLN* 2.3 61.8 + - - +
105U LEU* 1.3 71.1 - - - +
107U GLU* 1.3 58.8 + - - +
109U LEU* 3.0 27.6 + - + +
110U GLU* 4.2 2.4 + - - +
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Residues in contact with GLU 107 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69U ARG* 5.4 6.2 + - - -
100U ARG* 4.0 16.1 + - - -
103U GLN* 3.2 25.0 + - + +
104U ILE* 3.4 21.9 - - - +
106U ARG* 1.3 78.2 - - - +
108U ASN* 1.3 64.2 + - - +
110U GLU* 3.8 19.5 - - - +
111U HIS* 4.7 1.0 - - - -
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Residues in contact with ASN 108 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68U TYR* 3.5 28.6 - - - +
69U ARG 3.9 3.4 + - - +
71U LEU* 3.2 31.9 - - + +
104U ILE* 2.9 29.9 + - - +
105U LEU 3.4 0.7 - - - -
107U GLU* 1.3 81.6 - - - +
109U LEU* 1.3 67.9 + - - +
110U GLU* 3.2 2.5 - - - -
111U HIS* 2.8 22.4 + - - +
112U PHE* 3.1 31.3 - - + -
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Residues in contact with LEU 109 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88U VAL* 3.1 45.8 - - + +
89U GLU* 3.6 19.7 - - + +
91U VAL* 4.5 4.3 - - + -
92U LEU* 3.6 30.7 - - + -
105U LEU* 2.6 16.5 + - + +
106U ARG* 3.0 18.8 - - + +
108U ASN* 1.3 75.6 - - - +
110U GLU* 1.3 54.5 + - - +
111U HIS 2.4 15.4 + - - -
112U PHE* 2.5 37.7 + - + +
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Residues in contact with GLU 110 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54U LYS* 2.6 31.4 + - - -
106U ARG 4.2 1.2 + - - +
107U GLU 3.8 17.0 - - - +
109U LEU* 1.3 76.7 - - - +
111U HIS* 1.3 86.1 + - + +
112U PHE 4.6 1.1 - - - -
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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