Contacts of the helix formed by residues 105 - 114 (chain U) in PDB entry 1NJI
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 ASP 105 (chain U).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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80A A 4.4 8.1 + - - -
95A A 3.9 19.3 + - - +
97A G 2.6 39.5 + - - +
102U ASP 5.1 0.4 + - - +
103U LEU 3.0 4.0 - - - +
104U GLU* 1.3 79.5 - - - +
106U GLU* 1.3 65.6 + - - +
107U LYS* 2.7 30.8 + - - +
108U ARG* 3.5 27.2 + - + +
109U GLU* 3.1 22.7 + - - +
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Residues in contact with GLU 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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97A G 3.9 16.2 + - - +
104U GLU 3.8 4.3 + - - +
105U ASP* 1.3 74.9 + - - +
107U LYS* 1.3 57.5 + - + +
109U GLU* 3.4 10.3 + - - +
110U ALA* 2.7 37.9 + - - +
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Residues in contact with LYS 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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79A G 3.1 31.5 + - + +
97A G 3.6 60.0 + - + +
105U ASP* 2.7 22.2 + - - +
106U GLU* 1.3 74.0 - - + +
108U ARG* 1.3 63.6 + - - +
110U ALA* 3.2 7.0 + - - +
111U ARG* 3.0 40.2 + - - +
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Residues in contact with ARG 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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80A A 4.2 15.2 + - - +
40U VAL* 3.7 13.5 - - - +
41U ARG 3.2 8.9 + - - -
43U ASN* 2.8 42.0 - - - +
46U ASP* 2.8 39.0 + - - -
101U LEU* 3.5 18.1 - - - +
102U ASP 2.8 29.3 + - - +
103U LEU* 4.0 9.7 - - + +
105U ASP* 3.4 24.0 + - + +
107U LYS* 1.3 77.2 - - - +
109U GLU* 1.3 65.2 + - - +
111U ARG* 3.1 21.0 + - - +
112U LEU* 2.9 24.1 + - + +
119U ALA* 4.0 8.2 - - + +
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Residues in contact with GLU 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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35U TYR* 5.5 0.2 - - + -
103U LEU* 4.2 41.1 - - + +
105U ASP 3.1 14.4 + - - +
106U GLU* 3.7 9.0 - - - +
108U ARG* 1.3 78.5 - - - +
110U ALA* 1.3 64.0 + - - +
112U LEU* 3.2 8.4 + - - +
113U GLU* 3.0 47.7 + - - +
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Residues in contact with ALA 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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106U GLU 2.7 22.3 + - - +
107U LYS* 3.3 10.1 - - - +
109U GLU* 1.3 74.2 - - - +
111U ARG* 1.3 63.1 + - - +
113U GLU* 3.2 5.8 + - - +
114U SER* 2.9 26.2 + - - -
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Residues in contact with ARG 111 (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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79A G 3.5 58.9 + - - +
80A A 2.9 32.7 + - - -
97A G 5.3 0.6 - - - +
37U GLN* 3.9 0.2 - - - +
105U ASP* 4.6 2.0 + - - -
107U LYS* 3.0 21.4 + - - +
108U ARG* 3.4 29.5 - - - +
110U ALA* 1.3 76.2 - - + +
112U LEU* 1.3 52.9 + - - +
114U SER* 3.1 9.8 + - - -
117U ASP* 3.0 32.2 - - + +
118U SER 4.4 3.6 - - - -
119U ALA* 3.6 35.0 - - + +
8073U MG 2.6 27.2 - - - -
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Residues in contact with LEU 112 (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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27U LEU* 5.1 4.5 - - + -
35U TYR* 3.6 53.7 - - + +
37U GLN* 3.7 26.4 - - + +
40U VAL* 4.5 11.9 - - + -
101U LEU* 3.8 22.0 - - + -
103U LEU* 3.5 32.8 - - + -
108U ARG* 2.9 17.2 + - - +
109U GLU* 3.2 8.9 + - - +
111U ARG* 1.3 76.7 - - - +
113U GLU* 1.3 59.1 + - - +
119U ALA* 3.9 9.2 - - + +
8073U MG 2.4 19.3 - - - -
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Residues in contact with GLU 113 (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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34U GLU 6.0 0.2 - - - +
35U TYR* 3.9 30.2 + - + +
109U GLU* 3.0 40.2 + - - +
110U ALA* 3.8 4.9 - - - +
112U LEU* 1.3 76.8 - - - +
114U SER* 1.3 70.5 + - - +
115U GLU* 3.5 2.8 + - - +
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Residues in contact with SER 114 (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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35U TYR 5.0 1.0 - - - +
110U ALA 2.9 18.3 + - - -
111U ARG* 3.1 14.3 + - - -
112U LEU 3.4 0.2 - - - +
113U GLU* 1.3 77.3 - - - +
115U GLU* 1.3 58.2 + - - +
116U ASP* 4.2 4.9 - - - -
117U ASP* 3.4 21.9 + - - +
8073U MG 2.2 31.9 - - - -
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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