Contacts of the helix formed by residues 69 - 83 (chain L) in PDB entry 2NZV
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 69 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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29L PHE* 3.2 25.8 - - - +
30L ASP* 3.4 18.8 + - - +
31L SER* 2.4 41.6 + - - -
68L SER* 1.3 88.0 + - - +
70L GLU* 1.3 63.8 + - - +
71L ALA 3.6 2.2 - - - -
72L ASP* 3.5 21.9 + - + +
73L ALA* 3.1 15.2 + - - +
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Residues in contact with GLU 70 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2L ALA* 3.4 26.8 + - - +
31L SER* 3.3 2.9 + - - -
65L ALA* 3.4 27.8 - - + +
66L GLU* 2.8 20.9 - - - +
67L GLY 3.1 33.4 + - - +
68L SER 4.0 0.2 - - - -
69L ASP* 1.3 72.9 - - - +
71L ALA* 1.3 55.2 + - - +
73L ALA* 2.8 9.0 + - - +
74L LEU* 2.7 34.8 + - - +
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Residues in contact with ALA 71 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69L ASP 3.6 0.2 - - - -
70L GLU* 1.3 78.2 - - - +
72L ASP* 1.3 63.8 + - - +
74L LEU* 3.6 7.0 + - - +
75L ALA* 3.0 30.1 + - - +
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Residues in contact with ASP 72 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29L PHE* 2.9 30.4 - - + -
69L ASP* 3.7 27.7 - - + +
70L GLU 3.1 0.2 - - - -
71L ALA* 1.3 79.5 - - - +
73L ALA* 1.3 61.1 + - - +
75L ALA* 3.7 4.1 - - - +
76L ALA* 3.2 14.2 + - - +
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Residues in contact with ALA 73 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29L PHE* 3.4 33.4 - - + -
31L SER* 4.9 2.5 - - - -
33L ILE* 4.3 13.0 - - + -
65L ALA* 4.2 12.6 - - + -
69L ASP 3.1 10.4 + - - +
70L GLU* 2.8 9.8 + - - +
72L ASP* 1.3 75.9 - - - +
74L LEU* 1.3 59.2 + - - +
75L ALA 2.8 11.1 + - - -
76L ALA 3.3 1.4 + - - -
77L LEU* 3.1 30.4 + - + +
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Residues in contact with LEU 74 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2L ALA 3.7 15.9 - - - +
3L GLN 3.4 30.5 - - - +
4L LYS* 3.4 26.4 - - + +
63L ILE* 3.1 40.4 - - + +
65L ALA* 4.5 6.8 - - + +
70L GLU 2.7 20.0 + - - +
71L ALA* 3.8 6.7 - - - +
73L ALA* 1.3 72.2 - - - +
75L ALA* 1.3 56.4 + - - +
77L LEU* 4.4 7.9 - - - +
78L GLU* 3.2 26.4 + - - +
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Residues in contact with ALA 75 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71L ALA 3.0 18.4 + - - +
72L ASP* 3.7 6.5 - - - +
73L ALA 2.8 2.2 + - - -
74L LEU* 1.3 77.9 - - - +
76L ALA* 1.3 65.2 + - - +
77L LEU 3.2 1.6 - - - -
78L GLU* 3.1 22.1 + - - +
79L ASP* 3.2 12.5 - - - +
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Residues in contact with ALA 76 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29L PHE* 3.2 34.1 - - + -
72L ASP 3.2 3.5 + - - +
75L ALA* 1.3 76.2 - - - +
77L LEU* 1.3 54.0 + - - +
79L ASP* 3.1 15.7 + - + +
80L THR* 2.7 38.7 + - - +
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Residues in contact with LEU 77 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6L PHE* 5.5 1.3 - - + -
22L LEU* 4.1 22.8 - - + +
25L ALA* 2.9 34.1 - - + +
26L ALA* 4.5 7.6 - - + -
29L PHE* 4.8 4.0 - - + -
33L ILE* 3.8 20.6 - - + -
44L LEU* 4.8 4.3 - - + -
63L ILE* 3.4 36.6 - - + -
73L ALA* 3.1 27.2 + - + +
74L LEU* 4.6 4.5 - - + +
76L ALA* 1.3 74.6 - - - +
78L GLU* 1.3 56.8 + - + +
80L THR* 3.2 4.7 + - - -
81L MET* 2.8 33.6 + - - +
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Residues in contact with GLU 78 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4L LYS* 3.3 31.9 - - + +
6L PHE* 3.4 38.9 - - + -
74L LEU* 3.2 20.0 - - - +
75L ALA* 3.1 11.8 + - - +
77L LEU* 1.3 74.2 - - + +
79L ASP* 1.3 67.4 + - - +
81L MET* 3.2 3.4 + - - +
82L SER* 3.1 24.8 + - - -
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Residues in contact with ASP 79 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75L ALA* 3.2 16.8 - - - +
76L ALA* 3.1 16.1 + - + +
78L GLU* 1.3 78.6 - - - +
80L THR* 1.3 53.9 + - - +
81L MET 2.9 1.0 + - - -
82L SER* 3.2 5.8 + - - -
83L LYS* 2.7 65.9 + - + +
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Residues in contact with THR 80 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21L THR* 3.8 20.6 - - + -
22L LEU* 3.4 22.5 - - + +
25L ALA* 3.6 31.5 - - + +
76L ALA* 2.7 27.3 + - - +
77L LEU* 3.4 11.2 - - - -
79L ASP* 1.3 73.1 - - - +
81L MET* 1.3 56.6 + - - +
83L LYS* 4.0 5.2 - - - -
84L GLU* 2.9 33.2 + - + +
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Residues in contact with MET 81 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6L PHE* 3.4 40.8 - - + -
8L VAL* 5.9 0.4 - - + -
14L ILE* 4.9 2.7 - - + -
22L LEU* 4.0 16.6 - - + +
61L ILE* 4.3 20.4 - - + -
63L ILE* 5.5 5.2 - - + -
77L LEU 2.8 19.3 + - - +
78L GLU* 3.5 8.3 - - - +
79L ASP 2.9 1.0 + - - -
80L THR* 1.3 75.4 - - - +
82L SER* 1.3 58.5 + - - +
84L GLU* 3.2 2.9 + - - -
85L GLY 3.0 21.3 + - - -
86L LEU* 3.0 46.5 + - + +
87L GLY* 3.2 31.0 - - - +
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Residues in contact with SER 82 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78L GLU 3.1 13.8 + - - -
79L ASP* 3.3 8.5 + - - -
81L MET* 1.3 75.5 - - - +
83L LYS* 1.3 68.3 + - - +
84L GLU 3.2 1.3 + - - -
85L GLY* 3.5 12.1 + - - +
87L GLY 4.5 12.6 - - - -
88L GLU* 6.2 1.1 - - - -
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Residues in contact with LYS 83 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79L ASP* 2.7 55.2 + - + +
80L THR* 4.2 5.8 - - - +
82L SER* 1.3 78.4 + - - +
84L GLU* 1.3 71.6 + - + +
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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