Contacts of the helix formed by residues 66 - 80 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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43A SER* 3.1 23.1 + - - -
45A GLN* 4.2 5.0 + - - -
46A THR* 4.2 4.7 - - - -
62B ALA* 6.1 0.4 - - + -
64B ARG* 3.6 25.6 + - + +
65B VAL* 1.3 74.4 - - - +
67B VAL* 1.3 79.0 + - - +
68B ASP* 3.1 3.0 + - + +
69B GLN* 3.1 33.1 + - - +
70B LEU* 3.7 5.3 + - - +
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Residues in contact with VAL 67 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45A GLN* 4.3 20.6 - - + +
46A THR* 3.9 19.7 + - - +
49A ALA* 5.0 12.3 - - + -
66B ASP* 1.3 84.7 + - - +
68B ASP* 1.3 57.4 + - - +
70B LEU* 3.3 15.2 + - + +
71B GLU* 2.9 63.8 + - + +
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Residues in contact with ASP 68 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60B GLU* 5.0 3.0 - - - +
66B ASP* 3.1 1.7 + - + +
67B VAL* 1.3 75.2 - - - +
69B GLN* 1.3 76.3 + - - +
71B GLU* 3.4 12.1 + - - +
72B LYS* 3.1 36.8 + - - +
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Residues in contact with GLN 69 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53B GLY 4.3 5.8 - - - +
56B GLN* 3.6 26.9 - - + +
57B ALA* 3.5 25.8 - - + +
60B GLU* 2.9 29.5 + - - +
62B ALA* 3.7 25.0 - - - +
64B ARG 4.0 0.7 - - - +
65B VAL* 5.4 0.4 - - + -
66B ASP* 3.1 35.3 + - - +
68B ASP* 1.3 86.2 + - - +
70B LEU* 1.3 69.1 + - - +
72B LYS* 3.0 16.6 + - - +
73B VAL* 3.2 10.0 + - - +
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Residues in contact with LEU 70 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46A THR* 5.3 11.7 - - + -
49A ALA* 5.0 13.7 - - + -
50A ILE* 5.2 16.2 - - + -
53A LEU* 5.6 5.6 - - + -
49B ALA* 4.0 28.5 - - + +
50B ALA* 6.0 0.4 - - - -
53B GLY* 4.5 11.5 - - - -
65B VAL* 5.7 4.2 - - + +
66B ASP 3.7 5.1 + - - +
67B VAL* 3.3 20.1 + - + +
69B GLN* 1.3 78.8 - - - +
71B GLU* 1.3 54.2 + - + +
73B VAL* 2.8 19.1 + - + +
74B LEU* 2.7 60.0 + - + -
77B LEU* 5.4 1.6 - - + -
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Residues in contact with GLU 71 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67B VAL* 2.9 48.2 + - + +
68B ASP* 4.0 10.3 + - - +
69B GLN 3.2 0.2 - - - -
70B LEU* 1.3 78.6 - - + +
72B LYS* 1.3 56.5 + - - +
74B LEU* 3.7 25.5 - - + +
75B PRO* 3.0 22.9 - - - +
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Residues in contact with LYS 72 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56B GLN* 3.5 28.6 - - + +
60B GLU* 3.6 24.3 + - - +
68B ASP* 3.1 22.9 + - - +
69B GLN 3.0 10.9 + - - +
71B GLU* 1.3 77.5 - - - +
73B VAL* 1.3 56.7 + - - +
74B LEU 3.5 0.2 - - - -
75B PRO* 3.7 14.4 - - - +
76B GLN* 5.5 0.5 - - - +
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Residues in contact with VAL 73 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49B ALA* 5.0 1.1 - - - +
52B ARG* 3.8 45.2 - - + +
53B GLY 4.2 1.3 - - - +
56B GLN* 3.8 20.6 - - + +
69B GLN 3.2 9.3 + - - +
70B LEU* 2.8 31.5 + - + +
72B LYS* 1.3 77.4 - - - +
74B LEU* 1.3 59.9 + - + +
75B PRO 3.3 2.0 - - - -
76B GLN* 3.2 15.7 + - + +
77B LEU* 2.9 28.5 + - + +
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Residues in contact with LEU 74 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53A LEU* 4.0 27.4 - - + -
70B LEU* 2.7 42.5 + - + +
71B GLU* 3.7 28.5 - - + +
73B VAL* 1.3 71.8 - - - +
75B PRO* 1.4 71.9 - - + +
77B LEU* 4.1 24.5 - - + +
78B LEU* 3.1 38.8 + - + +
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Residues in contact with PRO 75 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71B GLU 3.0 18.8 - - - +
72B LYS* 3.7 13.0 - - - +
73B VAL 3.5 1.3 - - - -
74B LEU* 1.4 95.2 - - + +
76B GLN* 1.3 62.2 + - - +
78B LEU* 4.0 1.3 - - + +
79B LEU* 3.1 33.4 + - + +
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Residues in contact with GLN 76 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52B ARG* 3.4 28.4 + - - +
72B LYS 5.5 0.4 - - - +
73B VAL* 3.2 22.6 + - + +
75B PRO* 1.3 79.3 - - - +
77B LEU* 1.3 61.5 + - - +
79B LEU* 3.7 21.7 + - - +
80B ASP* 3.4 29.9 + - - -
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Residues in contact with LEU 77 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53A LEU* 3.7 30.1 - - + -
45B PHE* 4.0 11.2 - - + +
48B GLU* 4.7 3.8 - - + -
49B ALA* 3.8 41.7 - - + +
52B ARG* 4.6 11.6 - - + +
70B LEU* 5.4 2.0 - - + -
73B VAL* 2.9 19.7 + - + +
74B LEU* 3.9 17.0 - - + +
75B PRO 3.3 0.2 - - - -
76B GLN* 1.3 73.3 - - - +
78B LEU* 1.3 61.6 + - + +
80B ASP* 3.3 4.7 + - + +
81B PHE* 3.2 63.5 + - + -
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Residues in contact with LEU 78 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53A LEU* 5.1 15.3 - - + -
57A GLN* 2.8 39.0 - - - +
60A ASN* 5.0 4.0 - - - +
45B PHE* 5.1 2.9 - - + -
74B LEU* 3.1 34.7 + - + +
75B PRO* 4.5 1.3 - - + +
77B LEU* 1.3 84.9 - - + +
79B LEU* 1.3 59.1 + - - +
81B PHE* 3.2 24.0 - - + +
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Residues in contact with LEU 79 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88A ARG* 3.3 19.9 + - - -
75B PRO* 3.1 28.4 + - + +
76B GLN* 3.7 30.3 - - - +
78B LEU* 1.3 75.9 - - - +
80B ASP* 1.3 63.1 + - - +
81B PHE 3.1 1.6 - - - -
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Residues in contact with ASP 80 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88A ARG* 2.3 39.6 - - - +
89A SER* 3.4 28.4 + - - +
92A LEU* 5.5 0.2 - - - +
52B ARG* 2.8 37.5 + - - +
76B GLN* 3.4 21.9 + - - +
77B LEU* 3.3 11.2 + - + +
79B LEU* 1.3 76.8 - - - +
81B PHE* 1.3 76.3 + - + +
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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