Contacts of the helix formed by residues 62 - 74 (chain D) 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 GLU 62 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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25D VAL* 3.3 34.0 - - + +
28D ARG* 2.5 35.6 + - - -
60D TYR* 4.1 1.4 - - - +
61D ASP* 1.3 90.2 + - - +
63D ASP* 1.3 61.1 + - - +
64D GLU* 4.4 3.6 - - + +
65D VAL* 3.5 23.8 - - + +
66D LEU* 2.9 28.4 + - - +
281E LYS* 5.9 4.0 - - - +
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Residues in contact with ASP 63 (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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61D ASP 3.1 7.0 + - - +
62D GLU* 1.3 70.0 - - - +
64D GLU* 1.3 57.2 + - - +
66D LEU* 3.1 4.3 + - - +
67D LEU* 2.6 36.9 + - - +
99D VAL* 3.6 16.3 - - - +
101D GLU* 3.5 25.6 - - + +
104D VAL* 3.5 12.2 - - + +
246E LYS* 4.2 1.9 + - - -
281E LYS* 4.7 11.9 + - - +
282E TYR* 4.6 5.5 + - - -
307F TYR* 2.8 30.6 + - + +
308F PHE* 3.8 17.9 - - + -
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Residues in contact with GLU 64 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25D VAL* 4.8 4.8 - - + +
29D LEU* 3.7 29.0 - - + +
33D LYS* 5.4 5.1 + - - -
62D GLU* 3.2 5.1 - - + +
63D ASP* 1.3 80.3 - - - +
65D VAL* 1.3 62.7 + - + +
67D LEU* 3.5 5.0 - - + +
68D ALA* 3.4 13.5 + - - +
307F TYR* 5.5 0.2 - - - -
308F PHE* 3.3 40.3 - - + +
309F LEU* 2.6 56.5 + - - +
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Residues in contact with VAL 65 (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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25D VAL* 4.4 10.1 - - + -
28D ARG* 4.9 5.4 - - - -
29D LEU* 3.2 34.5 - - + +
32D ILE* 4.2 20.4 - - + -
60D TYR* 3.8 31.0 - - + -
62D GLU* 3.2 31.7 + - + +
63D ASP 3.1 0.6 - - - -
64D GLU* 1.3 74.7 - - - +
66D LEU* 1.3 69.2 + - + +
68D ALA* 2.8 14.9 + - - +
69D LEU* 2.9 12.9 + - + -
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Residues in contact with LEU 66 (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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59D ILE* 5.9 2.7 - - + -
60D TYR* 3.8 39.9 - - + +
61D ASP* 3.7 15.5 - - - +
62D GLU 2.9 18.1 + - - +
63D ASP* 3.5 5.6 - - - +
65D VAL* 1.3 77.8 - - + +
67D LEU* 1.3 64.0 + - - +
69D LEU* 3.2 10.2 + - + +
70D ALA* 3.0 24.3 + - - +
96D LEU* 3.7 17.6 - - + +
99D VAL* 3.8 29.4 - - + -
104D VAL* 3.8 13.7 - - + -
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Residues in contact with LEU 67 (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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63D ASP 2.6 21.1 + - - +
64D GLU* 3.5 9.0 - - + +
65D VAL 3.0 0.2 + - - -
66D LEU* 1.3 73.3 - - - +
68D ALA* 1.3 60.2 + - - +
70D ALA* 3.3 2.8 + - - +
71D GLU* 3.1 24.6 + - + +
103D VAL* 3.7 38.6 - - + +
104D VAL* 3.8 12.3 - - + +
107D LYS* 3.5 27.1 - - + -
304F THR* 5.8 3.1 - - + -
308F PHE* 3.9 20.2 - - + -
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Residues in contact with ALA 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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29D LEU* 4.6 2.7 - - + -
32D ILE* 3.9 15.7 - - + -
33D LYS* 4.1 28.9 - - + +
64D GLU 3.4 8.4 + - - +
65D VAL* 2.8 11.7 + - - +
67D LEU* 1.3 76.6 - - - +
69D LEU* 1.3 67.2 + - - +
70D ALA 3.0 1.7 + - - -
71D GLU* 3.0 8.1 + - - +
72D GLN* 2.8 27.2 + - - +
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Residues in contact with LEU 69 (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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32D ILE* 3.6 16.0 - - + +
35D LEU* 4.0 11.4 - - + -
55D LEU* 3.8 55.0 - - + +
60D TYR* 5.0 9.2 - - + -
65D VAL* 2.9 13.6 + - + +
66D LEU* 3.2 18.6 + - + +
68D ALA* 1.3 75.7 - - - +
70D ALA* 1.3 61.3 + - - +
72D GLN* 3.4 1.9 + - - +
73D LEU* 3.1 44.6 + - + +
92D PRO* 4.8 4.3 - - + -
96D LEU* 4.0 19.1 - - + -
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Residues in contact with ALA 70 (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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66D LEU 3.0 10.2 + - - +
67D LEU* 3.4 9.4 - - - +
69D LEU* 1.3 76.9 - - - +
71D GLU* 1.3 66.2 + - - +
72D GLN 3.2 0.9 + - - -
73D LEU 3.6 6.2 + - - -
74D GLY 3.7 1.2 + - - -
93D LEU* 4.2 4.4 - - - +
96D LEU* 3.3 26.4 - - + +
104D VAL 4.3 5.2 - - - +
107D LYS* 3.8 16.6 - - + -
108D ALA* 3.9 12.8 - - - +
111D SER* 3.1 19.4 + - - -
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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
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67D LEU* 3.1 12.3 + - + +
68D ALA* 3.0 10.4 + - - +
70D ALA* 1.3 76.9 - - - +
72D GLN* 1.3 75.3 + - - +
74D GLY* 3.7 7.1 + - - -
75D THR* 4.1 12.1 - - + +
107D LYS* 3.3 39.0 - - + +
110D GLU* 5.3 0.2 - - - +
111D SER* 4.4 1.9 + - - -
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Residues in contact with GLN 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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32D ILE 3.8 9.7 - - - +
33D LYS* 3.7 18.0 + - - +
35D LEU* 3.5 31.2 - - + -
36D SER* 2.8 37.1 + - - -
68D ALA* 2.8 17.0 + - - +
69D LEU* 3.5 8.3 - - - +
71D GLU* 1.3 86.2 + - - +
73D LEU* 1.3 57.3 + - - +
74D GLY 2.8 11.8 + - - -
75D THR* 2.8 34.6 + - - +
76D PHE* 3.5 11.9 - - + -
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Residues in contact with LEU 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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35D LEU* 4.4 7.2 - - + -
52D LEU* 4.2 16.4 - - + -
55D LEU* 4.1 24.0 - - + -
69D LEU* 3.1 31.3 + - + +
70D ALA 3.6 2.4 + - - +
72D GLN* 1.3 74.2 - - - +
74D GLY* 1.3 58.6 + - - +
75D THR 3.1 1.9 + - - -
76D PHE* 3.6 13.6 + - + -
89D LEU* 3.2 31.6 - - + +
92D PRO* 3.3 37.7 - - + -
93D LEU* 4.2 24.6 - - + +
96D LEU* 4.2 4.5 - - + -
115D ILE* 4.3 2.6 - - - +
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Residues in contact with GLY 74 (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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70D ALA 3.7 3.8 + - - -
71D GLU 3.7 6.6 + - - -
72D GLN 2.8 3.4 + - - -
73D LEU* 1.3 78.6 - - - +
75D THR* 1.3 63.9 + - - +
77D THR* 4.2 3.1 + - - -
111D SER* 3.6 28.5 + - - -
114D ALA* 4.7 7.9 - - - +
115D ILE* 3.6 20.3 - - - +
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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