Contacts of the helix formed by residues 57 - 74 (chain E) in PDB entry 1NVI
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 GLY 57 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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57D GLN* 3.4 14.3 - - - +
56E PRO* 1.3 71.1 - - - +
58E MET* 1.3 61.7 + - - -
59E THR 3.2 0.7 - - - -
60E GLU* 2.9 22.6 + - - +
61E LYS* 3.2 22.2 + - - +
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Residues in contact with MET 58 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54D ALA* 3.7 15.7 - - + -
57D GLN* 3.2 42.1 + - + +
58D THR* 4.2 0.2 - - - -
59D LEU* 3.7 44.0 - - + +
75D PHE* 4.6 3.4 - - + -
55E TYR* 3.5 42.6 - - + -
56E PRO 3.2 5.9 + - - -
57E GLY* 1.3 75.2 - - - +
59E THR* 1.3 58.0 + - - +
61E LYS* 3.6 2.4 - - - +
62E ALA* 2.8 33.3 + - + +
121E ARG 4.8 2.5 - - - +
123E PRO* 3.7 20.0 - - + -
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Residues in contact with THR 59 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8E VAL* 4.5 3.7 - - - +
54E HIS* 3.1 21.4 + - + -
55E TYR 2.8 33.2 + - - +
58E MET* 1.3 75.6 - - - +
60E GLU* 1.3 76.8 + - - +
62E ALA* 3.3 1.7 + - - +
63E LEU* 3.0 31.4 + - - +
122E ALA* 5.4 0.2 - - - +
123E PRO* 2.9 45.2 - - + +
124E PHE* 4.4 15.0 - - + -
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Residues in contact with GLU 60 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6E ILE* 4.4 12.3 - - + +
8E VAL* 4.0 33.9 - - + +
54E HIS* 4.6 6.6 - - - -
56E PRO* 5.1 0.5 - - - +
57E GLY* 2.9 32.8 + - - +
59E THR* 1.3 83.0 + - - +
61E LYS* 1.3 57.3 + - - +
63E LEU* 3.4 6.1 + - - +
64E ALA* 3.0 28.8 + - - +
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Residues in contact with LYS 61 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56D ASN 4.1 4.6 + - - -
57D GLN* 3.0 48.9 - - + +
58D THR* 3.6 13.7 + - - -
57E GLY 3.2 14.8 + - - +
58E MET 3.6 2.5 - - - +
60E GLU* 1.3 78.4 - - - +
62E ALA* 1.3 64.6 + - - +
64E ALA* 3.3 7.5 + - - +
65E GLU* 3.0 52.4 + - + +
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Residues in contact with ALA 62 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57D GLN 6.0 0.4 - - - +
58E MET* 2.8 26.5 + - + +
59E THR 3.6 4.5 - - - +
61E LYS* 1.3 74.0 - - - +
63E LEU* 1.3 56.8 + - - +
65E GLU* 3.1 15.0 + - - +
66E ILE* 3.0 34.7 + - + +
121E ARG* 4.0 13.0 - - + +
122E ALA* 4.3 5.2 - - - -
123E PRO* 3.9 20.4 - - + -
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Residues in contact with LEU 63 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6E ILE* 3.8 26.9 - - + -
7E VAL 5.1 1.3 - - - +
8E VAL* 3.7 30.5 - - + -
59E THR 3.0 17.8 + - - +
60E GLU 3.8 0.9 - - - +
62E ALA* 1.3 76.0 - - - +
64E ALA* 1.3 63.6 + - - +
66E ILE* 3.3 13.4 + - + +
67E VAL* 3.1 26.2 + - - +
81E VAL* 4.2 17.2 - - + +
83E HIS* 4.6 12.1 - - + -
114E ILE* 6.4 1.1 - - + -
118E LEU* 3.7 28.7 - - + -
122E ALA* 4.1 19.1 - - + -
124E PHE* 4.6 4.5 - - + -
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Residues in contact with ALA 64 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4E THR* 6.0 1.3 - - - -
6E ILE* 4.6 16.9 - - + +
60E GLU 3.0 17.4 + - - +
61E LYS* 3.6 7.9 - - - +
63E LEU* 1.3 77.6 - - - +
65E GLU* 1.3 56.7 + - + +
67E VAL* 3.5 4.3 + - - +
68E ASP* 3.0 35.6 + - - +
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Residues in contact with GLU 65 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57D GLN 5.1 1.9 - - - +
58D THR* 4.6 8.2 + - - +
61E LYS* 3.0 53.2 + - + +
62E ALA* 3.1 15.0 + - - +
64E ALA* 1.3 73.7 - - + +
66E ILE* 1.3 66.5 + - + +
68E ASP* 3.3 12.1 + - - +
69E GLU* 3.0 23.4 + - - +
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Residues in contact with ILE 66 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62E ALA 3.0 24.1 + - - +
63E LEU* 3.3 17.4 + - + +
65E GLU* 1.3 77.3 - - + +
67E VAL* 1.3 61.7 + - - +
69E GLU* 3.3 7.3 + - - +
70E ALA* 3.0 20.8 + - - +
113E PHE* 3.9 4.9 - - + -
114E ILE* 3.9 32.1 - - + +
117E TYR* 3.8 35.9 - - + +
118E LEU* 3.8 28.7 - - + +
121E ARG* 4.5 13.9 - - + -
122E ALA 4.8 4.0 - - - +
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Residues in contact with VAL 67 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4E THR* 3.7 23.3 - - + +
6E ILE* 4.0 9.0 - - + -
63E LEU 3.1 15.2 + - - +
64E ALA* 3.9 4.7 - - - +
66E ILE* 1.3 76.3 - - - +
68E ASP* 1.3 65.5 + - - +
70E ALA* 3.1 7.9 + - + +
71E ARG* 2.9 41.4 + - + +
79E VAL* 3.9 20.9 - - + -
81E VAL* 3.8 27.8 - - + -
114E ILE* 4.3 9.4 - - + -
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Residues in contact with ASP 68 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64E ALA* 3.0 22.2 + - - +
65E GLU* 3.4 15.0 - - - +
66E ILE 3.3 0.2 - - - -
67E VAL* 1.3 78.2 - - - +
69E GLU* 1.3 60.4 + - - +
71E ARG* 3.2 15.0 + - - +
72E ASN* 3.2 27.3 + - - +
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Residues in contact with GLU 69 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65E GLU 3.0 12.5 + - - +
66E ILE* 3.7 9.9 - - - +
67E VAL 3.3 0.2 - - - -
68E ASP* 1.3 73.4 - - - +
70E ALA* 1.3 66.3 + - - +
72E ASN* 3.1 29.3 + - - +
73E ARG* 3.0 40.8 + - - +
113E PHE* 3.7 22.7 - - + -
117E TYR* 4.6 9.4 - - + -
121E ARG* 5.9 0.9 - - - +
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Residues in contact with ALA 70 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66E ILE 3.0 13.8 + - - +
67E VAL 3.1 8.7 + - - +
69E GLU* 1.3 74.8 - - - +
71E ARG* 1.3 58.9 + - - +
73E ARG 3.1 1.7 + - - -
74E TRP* 2.9 43.4 + - + +
76E LEU* 4.0 16.2 - - + -
110E ALA* 4.7 1.3 - - + -
113E PHE* 3.9 22.4 - - + -
114E ILE* 4.0 17.7 - - + -
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Residues in contact with ARG 71 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2E ALA 3.5 18.9 + - - +
3E GLU 3.1 13.9 + - - -
4E THR* 2.9 29.2 + - - -
67E VAL* 2.9 24.8 + - + +
68E ASP* 3.5 15.9 - - - +
69E GLU 3.2 0.2 - - - -
70E ALA* 1.3 77.9 - - - +
72E ASN* 1.3 61.3 + - - +
74E TRP 3.0 19.7 - - - +
75E PRO* 5.1 0.2 - - - +
76E LEU* 3.2 29.0 + - + +
77E GLY 2.8 29.9 + - - -
79E VAL* 3.7 15.2 - - - +
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Residues in contact with ASN 72 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68E ASP* 3.2 15.9 + - - +
69E GLU* 3.1 28.8 + - - +
71E ARG* 1.3 78.9 + - - +
73E ARG* 1.3 61.6 + - - +
74E TRP 5.2 0.2 - - - -
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Residues in contact with ARG 73 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69E GLU* 3.0 36.4 + - - +
70E ALA 3.1 2.1 + - - +
72E ASN* 1.3 80.3 - - + +
74E TRP* 1.3 102.5 + - + +
75E PRO* 4.7 1.0 - - - +
113E PHE* 3.7 18.2 - - - -
117E TYR* 3.9 13.7 + - - -
150E TRP* 3.0 44.0 + - - +
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Residues in contact with TRP 74 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70E ALA* 2.9 27.2 + - - +
71E ARG* 3.0 23.1 - - - +
72E ASN 5.2 0.2 - - - -
73E ARG* 1.3 107.6 + - + +
75E PRO* 1.3 68.4 - - + +
76E LEU* 3.1 25.8 + - + +
106E SER* 3.6 29.4 - - - -
109E GLU* 2.9 41.1 + - + +
110E ALA* 3.7 14.4 - - + -
113E PHE* 3.5 50.0 - + + -
150E TRP* 3.8 17.7 - + - -
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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