Contacts of the helix formed by residues 73 - 81 (chain H) 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 VAL 73 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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48H GLU 5.6 0.2 - - - +
49H ALA 4.6 5.6 - - - +
52H ARG* 3.1 39.3 - - + +
53H GLY* 3.7 20.2 - - - +
56H GLN* 3.6 17.5 - - + +
69H GLN 3.1 9.4 + - - +
70H LEU* 2.9 26.8 + - + +
72H LYS* 1.3 78.6 - - - +
74H LEU* 1.3 56.7 + - + +
75H PRO* 3.7 1.3 - - - -
76H GLN* 3.7 9.8 + - + +
77H LEU* 2.8 36.4 + - + +
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Residues in contact with LEU 74 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53G LEU* 4.6 16.8 - - + -
70H LEU* 2.9 38.7 + - + +
71H GLU* 3.4 32.1 + - + +
73H VAL* 1.3 75.1 - - + +
75H PRO* 1.4 73.2 - - + +
77H LEU* 4.0 19.5 - - + -
78H LEU* 3.0 46.6 + - + +
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Residues in contact with PRO 75 (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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72D LYS* 3.9 26.7 - - + +
75D PRO* 4.5 11.7 - - + +
76D GLN* 5.1 11.7 + - + +
71H GLU 3.3 15.9 - - - +
72H LYS* 4.0 8.1 - - - +
73H VAL 3.8 1.1 - - - -
74H LEU* 1.4 89.5 - - + +
76H GLN* 1.3 57.1 + - - +
78H LEU* 4.0 2.0 - - + +
79H LEU* 3.1 33.1 + - - +
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Residues in contact with GLN 76 (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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75D PRO* 5.2 3.1 - - - +
52H ARG* 3.9 22.9 + - - +
72H LYS 5.2 2.2 + - - +
73H VAL* 3.7 14.3 + - + +
74H LEU 3.4 0.4 - - - -
75H PRO* 1.3 79.5 - - - +
77H LEU* 1.3 59.1 + - - +
79H LEU* 3.5 24.7 - - - +
80H ASP* 3.3 32.3 + - - +
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Residues in contact with LEU 77 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53G LEU* 4.5 11.9 - - + -
45H PHE* 5.3 0.9 - - + +
48H GLU* 4.0 9.2 - - + +
49H ALA* 3.7 42.4 - - + +
52H ARG* 4.9 14.3 - - + +
70H LEU* 5.3 0.7 - - + -
73H VAL* 2.8 25.2 + - + +
74H LEU* 3.3 24.8 + - + +
76H GLN* 1.3 72.7 - - - +
78H LEU* 1.3 66.0 + - + +
80H ASP* 3.4 5.3 + - + +
81H PHE* 3.0 60.2 + - + +
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Residues in contact with LEU 78 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76D GLN* 4.1 14.6 - - - +
79D LEU* 3.1 15.1 - - - +
53G LEU* 4.5 18.8 - - + -
57G GLN* 3.6 31.4 - - - +
45H PHE* 4.9 7.0 - - + -
74H LEU* 3.0 39.3 + - + +
75H PRO* 4.4 1.1 - - + +
77H LEU* 1.3 82.5 - - + +
79H LEU* 1.3 64.8 + - - +
81H PHE* 3.4 20.7 - - + +
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Residues in contact with LEU 79 (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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75D PRO* 3.2 55.6 - - + +
78D LEU* 5.5 6.1 - - + -
79D LEU* 3.0 42.0 - - + +
88G ARG* 3.8 17.7 + - - +
75H PRO 3.1 13.8 + - - +
76H GLN* 3.5 33.4 - - - +
78H LEU* 1.3 75.4 - - - +
80H ASP* 1.4 60.4 + - - +
81H PHE 3.5 1.0 + - - -
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Residues in contact with ASP 80 (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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88G ARG* 3.5 20.5 - - - +
89G SER* 3.1 34.5 + - - +
92G LEU* 3.8 11.1 - - - +
52H ARG* 3.0 39.0 + - - +
76H GLN* 3.3 23.6 + - - +
77H LEU* 3.4 6.5 + - + +
79H LEU* 1.4 78.1 - - - +
81H PHE* 1.3 73.1 + - + +
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Residues in contact with PHE 81 (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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79D LEU* 6.0 0.4 - - - -
57G GLN* 3.9 27.9 + - - +
61G PHE* 4.3 16.7 - + + -
85G LEU 5.1 4.7 - - - +
88G ARG* 4.7 9.9 - - - +
92G LEU* 3.4 33.4 - - + -
41H LEU* 4.2 16.8 - - + -
44H VAL* 4.0 7.9 - - + -
45H PHE* 3.5 54.1 - + + -
48H GLU* 4.4 9.2 - - + -
77H LEU* 3.0 46.8 + - + +
78H LEU* 3.4 20.0 - - + -
79H LEU 3.3 3.1 - - - -
80H ASP* 1.3 87.5 - - + +
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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