Contacts of the helix formed by residues 66 - 81 (chain D) in PDB entry 4NE1
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 66 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43C SER* 3.5 9.5 - - - -
45C GLN* 3.4 25.3 + - - +
46C THR* 3.8 3.4 + - - -
64D ARG* 3.2 8.1 + - + +
65D VAL* 1.3 74.5 - - - +
67D VAL* 1.4 82.5 + - - +
68D ASP* 3.4 10.9 + - + +
69D GLN* 2.8 31.8 + - - +
70D LEU 3.7 4.2 + - - -
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Residues in contact with VAL 67 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45C GLN* 3.3 46.8 - - + +
46C THR* 5.1 0.4 - - - -
49C ALA* 4.7 8.1 - - + -
66D ASP* 1.4 83.7 + - - +
68D ASP* 1.3 55.7 + - - +
69D GLN 3.2 0.3 + - - -
70D LEU* 3.6 4.7 + - + +
71D GLU* 2.9 71.9 + - + +
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Residues in contact with ASP 68 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60D GLU* 4.4 1.3 - - - +
66D ASP* 3.4 10.2 + - + +
67D VAL* 1.3 75.9 - - - +
69D GLN* 1.3 74.1 + - - +
71D GLU* 4.1 6.1 + - - +
72D LYS* 3.1 53.9 + - - +
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Residues in contact with GLN 69 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56D GLN* 3.0 31.0 - - + +
57D ALA* 3.1 35.2 - - - +
60D GLU* 2.4 41.7 + - - +
62D ALA* 3.9 10.9 - - - +
64D ARG 3.8 3.8 - - - +
65D VAL* 3.7 5.8 - - + -
66D ASP* 2.8 41.1 + - - +
67D VAL 3.3 0.4 - - - -
68D ASP* 1.3 80.3 - - - +
70D LEU* 1.3 70.1 + - - +
71D GLU 3.2 0.9 - - - -
72D LYS 2.9 12.8 + - - -
73D VAL* 3.2 5.4 - - - +
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Residues in contact with LEU 70 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45C GLN 4.1 0.4 - - - +
46C THR* 3.3 62.6 - - + +
49C ALA* 3.4 23.6 - - + -
50C ILE* 3.8 14.8 - - + +
49D ALA 3.9 16.4 - - - +
53D GLY* 3.9 10.5 - - - -
56D GLN* 4.4 0.6 - - - +
65D VAL* 4.4 1.4 - - - +
66D ASP 3.7 2.3 + - - +
67D VAL* 3.6 8.0 + - + +
69D GLN* 1.3 77.7 - - - +
71D GLU* 1.3 49.9 + - + +
73D VAL* 2.8 21.4 + - + +
74D LEU* 2.7 46.8 + - + +
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Residues in contact with GLU 71 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49C ALA* 5.5 2.7 - - + +
67D VAL* 2.9 51.5 + - + +
68D ASP* 4.3 5.3 + - - +
70D LEU* 1.3 68.3 - - + +
72D LYS* 1.3 53.4 + - + +
73D VAL 3.1 4.9 - - - -
74D LEU* 3.6 23.2 - - + +
75D PRO* 2.6 30.3 - - - +
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Residues in contact with LYS 72 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56D GLN* 3.4 31.8 - - - +
60D GLU* 4.2 10.9 + - - +
68D ASP* 3.1 41.3 + - - +
69D GLN 2.9 2.2 + - - -
71D GLU* 1.3 77.7 - - - +
73D VAL* 1.3 59.6 + - - +
75D PRO* 3.7 9.9 - - - +
76D GLN* 5.2 1.6 + - - +
75H PRO* 3.9 26.7 - - + +
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Residues in contact with VAL 73 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49D ALA 4.8 2.0 - - - +
52D ARG* 3.7 34.1 - - + +
53D GLY 4.4 1.8 - - - +
56D GLN* 3.4 29.8 - - + +
69D GLN 3.2 16.2 - - - +
70D LEU* 2.8 36.0 + - + +
72D LYS* 1.3 77.4 - - - +
74D LEU* 1.3 64.5 + - + +
75D PRO* 3.4 2.2 - - - -
76D GLN* 3.8 7.9 + - - +
77D LEU* 3.3 21.7 + - + +
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Residues in contact with LEU 74 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49C ALA* 4.3 27.6 - - + +
50C ILE* 5.7 1.3 - - + -
53C LEU* 4.0 14.6 - - + -
70D LEU* 2.7 43.1 + - + +
71D GLU* 3.8 23.8 - - + -
73D VAL* 1.3 71.9 - - + +
75D PRO* 1.4 74.5 - - + +
77D LEU* 3.2 37.4 + - + +
78D LEU* 3.3 22.5 + - + +
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Residues in contact with PRO 75 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71D GLU 2.6 31.0 - - - +
72D LYS* 3.7 12.1 - - - +
73D VAL 3.5 2.7 - - - -
74D LEU* 1.4 85.2 - - + +
76D GLN* 1.3 61.6 + - - +
77D LEU 3.4 0.2 + - - -
78D LEU* 3.6 11.1 + - + +
79D LEU* 3.7 4.2 + - - +
75H PRO* 4.5 13.0 - - + +
76H GLN* 5.2 2.7 - - - +
79H LEU* 3.2 50.8 - - + +
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Residues in contact with GLN 76 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52D ARG* 4.1 16.5 + - - +
72D LYS 5.7 1.8 - - - +
73D VAL* 3.8 9.6 + - - +
74D LEU 3.5 0.2 - - - -
75D PRO* 1.3 78.1 - - + +
77D LEU* 1.3 61.8 - - - +
78D LEU 3.4 0.2 - - - -
79D LEU* 3.6 27.5 + - + +
80D ASP* 3.5 45.8 + - - +
75H PRO* 5.1 11.1 - - + +
78H LEU* 4.1 16.6 - - - +
79H LEU* 4.4 0.6 + - - +
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Residues in contact with LEU 77 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50C ILE* 6.4 0.2 - - - -
53C LEU* 3.4 30.5 - - + -
45D PHE* 4.3 5.6 - - + -
49D ALA* 3.4 41.7 - - + +
52D ARG* 4.2 21.1 - - - +
73D VAL* 3.3 18.6 + - + +
74D LEU* 3.2 24.2 + - + +
75D PRO 3.2 1.4 - - - -
76D GLN* 1.3 77.1 - - - +
78D LEU* 1.3 61.7 + - - +
80D ASP* 3.8 0.7 + - - +
81D PHE* 3.4 44.5 + - + +
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Residues in contact with LEU 78 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53C LEU* 3.3 43.7 - - + -
56C ARG* 5.4 5.8 - - - +
57C GLN* 4.3 12.3 - - - +
45D PHE* 5.9 0.7 - - + -
74D LEU* 3.3 18.8 + - + +
75D PRO* 4.1 7.2 - - + +
76D GLN 3.4 0.4 - - - -
77D LEU* 1.3 76.8 - - - +
79D LEU* 1.3 59.0 + - - +
80D ASP 3.4 0.2 - - - -
81D PHE 3.1 24.7 - - - +
79H LEU* 5.5 5.2 - - + -
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Residues in contact with LEU 79 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88C ARG* 5.3 6.8 + - - -
75D PRO 3.7 9.6 - - - +
76D GLN* 3.8 34.5 - - - +
77D LEU 3.4 0.4 - - - -
78D LEU* 1.3 79.9 - - - +
80D ASP* 1.3 62.9 + - - +
81D PHE* 4.8 0.9 - - - -
88G ARG* 4.3 18.4 - - - +
78H LEU 3.1 24.7 - - - +
79H LEU* 3.0 52.0 - - + +
81H PHE 6.0 0.4 - - - -
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Residues in contact with ASP 80 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89C SER* 5.3 11.0 + - - +
92C LEU* 5.1 5.9 - - - +
52D ARG* 3.5 34.8 + - - +
76D GLN* 3.5 30.0 + - - +
77D LEU 3.8 2.7 + - - +
79D LEU* 1.3 81.0 - - - +
81D PHE* 1.3 73.0 + - + +
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Residues in contact with PHE 81 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57C GLN* 3.1 34.3 + - - +
61C PHE* 4.1 19.1 - + - -
85C LEU 6.1 0.4 - - - -
92C LEU* 3.9 26.9 - - + -
41D LEU* 4.1 14.6 - - + -
44D VAL* 4.5 10.1 - - + -
45D PHE* 3.2 56.8 - + + -
48D GLU* 4.7 6.1 - - + -
52D ARG* 4.4 12.8 - - - -
77D LEU* 3.4 31.8 + - + +
78D LEU 3.1 19.6 - - - +
79D LEU 3.3 0.9 - - - -
80D ASP* 1.3 85.7 - - + +
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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