Contacts of the helix formed by residues 58 - 69 (chain E) in PDB entry 2NPP
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 58 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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41E VAL* 6.2 4.0 - - + -
56E LYS* 3.1 22.4 - - + +
57E GLU* 1.3 82.3 - - - +
59E LYS* 1.3 59.6 + - + +
60E ARG 3.5 0.9 - - - -
61E ALA* 3.1 28.9 - - - +
62E ALA* 3.4 6.8 + - + +
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Residues in contact with LYS 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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41E VAL 5.4 0.2 - - - +
42E LEU* 2.9 39.5 - - + +
45E PHE* 3.1 27.8 - - + +
46E VAL* 3.3 10.1 - - - +
47E SER* 5.6 1.1 - - - +
57E GLU 2.9 7.6 + - - +
58E VAL* 1.3 73.8 - - + +
60E ARG* 1.3 63.1 + - - +
61E ALA 2.9 6.6 + - - -
62E ALA* 3.2 6.5 + - - +
63E LEU* 2.9 36.9 + - + +
88E MET* 4.5 7.0 - - - -
92E ASN* 3.1 24.7 + - - -
123E HIS* 3.2 43.1 - - + +
127E VAL* 5.2 0.4 - - - -
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Residues in contact with ARG 60 (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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57E GLU* 3.5 44.9 + - + +
58E VAL 3.5 1.0 - - - -
59E LYS* 1.3 76.5 - - - +
61E ALA* 1.3 52.6 + - - +
63E LEU* 4.7 2.0 - - - -
64E SER* 2.7 38.7 + - - +
122E PRO* 6.3 4.0 - - + -
123E HIS* 5.1 12.1 - - + +
126E LEU* 4.0 20.9 - - + +
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Residues in contact with ALA 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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57E GLU* 4.6 5.9 + - - +
58E VAL* 3.1 14.9 + - - +
59E LYS 2.9 1.0 + - - -
60E ARG* 1.3 75.9 - - - +
62E ALA* 1.3 52.5 + - - +
63E LEU 2.6 8.4 + - - -
64E SER* 3.1 6.3 + - - -
65E GLU* 2.6 46.3 + - + +
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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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38E GLN* 3.8 22.9 - - + +
41E VAL* 5.1 4.9 - - + -
42E LEU* 4.5 10.5 - - + +
58E VAL* 3.4 8.1 + - + +
59E LYS* 3.2 11.4 + - - +
61E ALA* 1.3 78.3 - - - +
63E LEU* 1.3 57.6 + - - +
65E GLU* 3.8 14.8 + - - +
66E MET* 2.8 35.7 + - - +
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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
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42E LEU* 3.5 30.1 - - + -
59E LYS* 2.9 32.3 + - + +
60E ARG* 5.0 0.7 - - - -
61E ALA 2.6 5.9 + - - -
62E ALA* 1.3 72.4 - - - +
64E SER* 1.3 58.1 + - - +
65E GLU 2.6 14.6 + - - -
66E MET* 2.7 19.6 + - + +
67E VAL* 3.0 16.6 + - + +
88E MET* 3.9 13.7 - - + -
123E HIS* 3.5 31.2 - - - +
126E LEU* 3.6 26.9 - - + -
127E VAL* 4.0 11.0 - - + +
130E PHE* 5.6 8.1 - - + -
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Residues in contact with SER 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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60E ARG* 2.7 27.1 + - - +
61E ALA* 3.2 5.4 + - - -
63E LEU* 1.3 76.8 - - - +
65E GLU* 1.3 60.2 + - - +
67E VAL* 3.5 9.8 - - - +
68E GLU* 2.9 46.8 + - - +
126E LEU* 4.1 14.8 - - - +
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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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38E GLN* 4.8 13.2 - - - +
61E ALA* 2.6 31.6 + - - +
62E ALA* 3.8 11.4 + - - +
63E LEU 2.6 4.6 + - - -
64E SER* 1.3 68.9 + - - +
66E MET* 1.3 59.6 + - - +
67E VAL 3.0 4.7 - - - -
68E GLU* 3.5 5.8 + - - +
69E TYR* 3.0 32.9 + - + +
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Residues in contact with MET 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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35E LYS* 4.1 17.3 - - + +
38E GLN* 4.0 12.1 - - + +
39E CYS* 3.3 46.2 - - + +
42E LEU* 5.3 0.9 - - - -
62E ALA 2.8 23.8 + - - +
63E LEU* 2.7 16.8 + - - +
65E GLU* 1.3 79.9 - - + +
67E VAL* 1.3 60.2 + - - +
69E TYR* 4.0 11.2 - - + -
70E ILE* 3.3 29.7 - - + +
82E TYR* 5.8 6.5 - - + -
85E VAL* 6.5 1.3 - - + -
88E MET* 6.5 0.2 - - - -
130E PHE* 3.7 34.5 - - + -
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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
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63E LEU* 3.2 17.9 - - + +
64E SER* 3.5 11.9 - - - +
65E GLU 3.0 0.4 - - - -
66E MET* 1.3 76.4 - - - +
68E GLU* 1.3 60.1 + - + +
69E TYR 2.9 3.6 - - - -
70E ILE* 2.7 27.6 + - - +
71E THR* 2.9 14.8 + - - +
126E LEU* 4.9 7.6 - - + +
129E GLU* 5.7 5.4 - - + -
130E PHE* 3.8 36.8 - - + +
133E ARG* 3.7 34.5 - - + +
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Residues in contact with GLU 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 SER* 2.9 33.8 + - - +
65E GLU* 4.1 5.4 + - - +
67E VAL* 1.3 83.6 - - + +
69E TYR* 1.3 56.5 + - - +
70E ILE 3.1 1.8 + - - -
71E THR* 3.9 9.2 - - - -
72E HIS* 3.6 26.7 + - + +
74E ARG* 3.2 20.1 + - - +
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Residues in contact with TYR 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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31E LEU* 4.0 22.2 - - + +
35E LYS* 5.2 13.8 - - + +
65E GLU* 3.0 21.1 + - + +
66E MET* 4.1 11.4 - - + +
67E VAL 2.9 0.8 + - - -
68E GLU* 1.3 76.4 - - - +
70E ILE* 1.3 73.3 + - + +
74E ARG* 3.0 27.7 - - + +
75E ASN* 3.0 33.4 + - - -
78E THR* 3.8 22.1 + - + +
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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