Contacts of the helix formed by residues 62 - 69 (chain H) 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 HIS 62 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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33H THR* 4.0 7.2 - - + -
37H THR* 3.0 34.7 + - + +
58H GLU 4.3 3.6 + - - -
59H ILE 3.3 27.6 + - - -
60H VAL* 2.7 7.4 + - - -
61H MET* 1.3 76.1 + - - +
63H ILE* 1.3 76.7 + - + +
64H PRO 3.3 0.6 - - - -
65H GLU* 3.7 4.2 + - - +
66H LEU* 3.0 31.7 + - + +
4N ALA* 4.1 12.9 - - + +
7N TYR* 3.5 52.1 - + + +
8N ILE* 6.0 1.1 - - + -
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Residues in contact with ILE 63 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33H THR* 4.6 7.2 - - + -
36H THR* 4.3 20.0 - - + -
37H THR* 4.1 9.6 - - - +
40H ILE* 4.5 10.7 - - + +
48H VAL* 4.4 19.3 - - + -
50H VAL* 3.3 27.4 - - + -
60H VAL* 2.8 37.5 + - + +
62H HIS* 1.3 91.0 - - + +
64H PRO* 1.3 77.6 - - + +
66H LEU* 3.5 3.7 - - + +
67H ALA* 2.8 22.7 + - + +
74H PHE* 4.8 4.9 - - + -
95H ALA* 4.8 2.0 - - + -
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Residues in contact with PRO 64 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3H TYR* 3.5 31.6 - - + +
5H ASP* 5.4 5.4 - - - +
60H VAL* 3.6 6.3 - - + +
61H MET 3.4 15.9 - - - +
63H ILE* 1.3 99.6 - - + +
65H GLU* 1.3 63.8 + - - +
67H ALA* 3.0 3.1 + - - +
68H ASP* 2.9 26.1 + - - +
74H PHE* 3.7 23.2 - - + -
76H PHE* 4.3 13.9 - - + -
19N GLN* 6.1 1.1 - - - +
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Residues in contact with GLU 65 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61H MET 5.0 1.9 + - - +
62H HIS* 3.7 5.5 + - - +
64H PRO* 1.3 78.1 - - - +
66H LEU* 1.3 63.4 + - - +
68H ASP* 3.0 14.2 + - + +
69H GLU* 3.0 39.4 + - + +
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Residues in contact with LEU 66 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37H THR* 3.9 27.6 - - + -
40H ILE* 3.6 28.7 - - + -
41H GLU* 4.2 9.2 - - + -
62H HIS* 3.0 31.7 + - + +
63H ILE* 3.5 3.1 - - + +
65H GLU* 1.3 77.9 + - - +
67H ALA* 1.3 64.0 + - - +
69H GLU* 3.3 32.1 + - - +
70H LYS* 3.3 25.5 + - + +
7N TYR* 3.8 24.7 - - + +
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Residues in contact with ALA 67 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40H ILE* 3.9 24.0 - - + +
48H VAL* 4.7 0.7 - - + -
63H ILE 2.8 16.2 + - - +
64H PRO 3.3 8.1 - - - +
66H LEU* 1.3 72.1 - - - +
68H ASP* 1.3 64.3 + - - +
70H LYS 3.0 9.7 + - - -
71H GLY 3.1 10.6 + - - -
72H VAL* 3.2 24.5 + - + +
74H PHE* 3.4 27.8 - - + -
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Residues in contact with ASP 68 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64H PRO* 2.9 24.6 + - - +
65H GLU* 3.0 13.4 + - + +
67H ALA* 1.3 76.9 - - - +
69H GLU* 1.3 57.9 + - - +
70H LYS 3.0 5.0 + - - -
71H GLY* 3.2 12.1 + - - +
72H VAL 5.0 1.3 - - - +
74H PHE* 3.6 19.9 - - - -
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Residues in contact with GLU 69 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65H GLU* 3.0 34.2 + - + +
66H LEU* 3.3 27.6 - - + +
68H ASP* 1.3 74.9 - - - +
70H LYS* 1.3 69.4 + - + +
71H GLY 3.6 0.4 - - - -
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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