Contacts of the helix formed by residues 64 - 77 (chain D) in PDB entry 2NPT
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 LYS 64 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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62D PRO* 3.9 33.9 - - - +
63D VAL* 1.3 73.6 - - - +
65D LEU* 1.3 66.3 + - - +
66D GLU* 4.2 7.2 - - + +
67D ASP* 2.9 35.7 + - - +
68D LEU* 3.2 13.2 + - - +
96D GLN* 3.2 20.0 - - - +
99D LEU* 3.6 4.0 - - - -
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Residues in contact with LEU 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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64D LYS* 1.3 70.5 - - - +
66D GLU* 1.3 57.8 + - - +
68D LEU* 3.2 17.5 + - + +
69D ARG* 2.9 37.3 + - + +
82D LEU* 4.4 9.6 - - + -
93D LEU* 3.8 26.2 - - + +
94D THR* 3.4 27.6 - - - +
95D THR 3.4 30.1 - - - +
96D GLN* 3.2 12.4 + - - +
99D LEU* 3.5 24.8 - - + +
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Residues in contact with GLU 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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64D LYS* 3.2 5.2 - - + +
65D LEU* 1.3 75.9 - - - +
67D ASP* 1.3 62.1 + - - +
69D ARG* 4.0 14.0 - - - +
70D SER* 2.9 46.9 + - - -
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Residues in contact with ASP 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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59D PHE* 3.9 18.4 - - + -
60D PRO 5.4 1.0 - - - +
62D PRO 4.2 2.9 - - - +
63D VAL* 3.9 3.8 - - - -
64D LYS* 2.9 43.4 + - - +
66D GLU* 1.3 76.8 - - - +
68D LEU* 1.3 66.5 + - - +
70D SER* 3.2 7.3 + - - -
71D LYS* 3.0 30.7 + - + +
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Residues in contact with LEU 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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46D VAL* 3.9 17.5 - - + -
48D PHE* 3.7 12.6 - - + -
59D PHE* 3.6 37.7 - - + -
63D VAL* 4.1 7.9 - - + -
64D LYS 3.2 7.8 + - - +
65D LEU* 3.2 9.7 + - + +
67D ASP* 1.3 79.5 - - - +
69D ARG* 1.4 57.7 + - - +
72D ALA* 2.9 30.5 + - - +
82D LEU* 3.4 27.4 - - + -
93D LEU* 4.9 0.2 - - + -
99D LEU* 3.7 36.3 - - + -
115D LEU* 4.9 2.0 - - + -
117D ILE* 4.7 12.6 - - + -
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Residues in contact with ARG 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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65D LEU* 2.9 31.2 + - + +
66D GLU* 3.7 20.4 - - - +
67D ASP 3.3 0.4 - - - -
68D LEU* 1.4 75.8 - - - +
70D SER* 1.3 57.9 + - - +
72D ALA* 3.3 4.3 + - - +
73D LYS* 2.9 28.3 + - - +
78D GLN 5.3 0.2 - - - +
79D SER* 5.7 1.6 - - - +
80D MET 4.8 11.5 + - - +
82D LEU* 4.0 27.4 - - + -
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Residues in contact with SER 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 GLU* 2.9 30.8 + - - +
67D ASP* 3.2 10.0 + - - -
69D ARG* 1.3 77.0 - - - +
71D LYS* 1.3 67.5 + - - +
73D LYS* 3.3 9.5 + - - +
74D ILE* 3.1 31.7 + - - +
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Residues in contact with LYS 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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48D PHE* 4.7 2.7 - - + -
57D LEU* 4.1 15.4 - - + +
59D PHE* 3.5 31.4 - - + -
67D ASP* 3.0 22.7 + - + +
68D LEU 4.1 0.9 - - - +
70D SER* 1.3 77.5 - - - +
72D ALA* 1.3 60.8 + - - +
74D ILE* 3.3 22.6 + - + +
75D ALA* 2.9 29.5 + - - +
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Residues in contact with ALA 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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48D PHE* 4.1 8.9 - - + -
68D LEU 2.9 19.8 + - - +
69D ARG* 3.6 6.7 - - - +
71D LYS* 1.3 75.3 - - - +
73D LYS* 1.3 57.9 + - - +
75D ALA* 3.3 6.9 + - - +
76D PHE* 2.9 33.1 + - - +
78D GLN 4.2 3.3 - - - +
80D MET* 4.3 8.3 - - + +
119D LEU* 3.7 38.1 - - + -
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Residues in contact with LYS 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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69D ARG 2.9 13.6 + - - +
70D SER* 3.5 12.8 - - - +
71D LYS 3.2 0.2 - - - -
72D ALA* 1.3 75.1 - - - +
74D ILE* 1.3 59.3 + - + +
77D GLY* 2.7 36.9 + - - -
78D GLN* 3.5 24.8 + - - +
79D SER* 4.2 27.2 - - - +
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Residues in contact with ILE 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 SER* 3.1 20.5 + - - +
71D LYS* 3.6 26.7 - - + +
73D LYS* 1.3 78.4 - - + +
75D ALA* 1.3 61.1 + - - +
76D PHE 3.7 0.2 + - - -
77D GLY* 4.4 1.7 + - - -
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Residues in contact with ALA 75 (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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77A GLU* 4.9 2.9 - - - +
48D PHE* 5.4 2.9 - - + -
55D ARG* 2.3 57.8 + - + +
57D LEU* 5.2 9.0 - - + -
71D LYS 2.9 17.4 + - - +
72D ALA* 3.8 6.5 - - - +
73D LYS 3.2 0.2 - - - -
74D ILE* 1.3 80.2 - - - +
76D PHE* 1.3 70.4 + - + +
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Residues in contact with PHE 76 (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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48D PHE* 4.3 7.9 - - + -
49D GLU 4.7 0.2 - - - -
50D HIS* 3.6 33.4 - + + -
53D GLU* 3.7 44.0 - - + -
55D ARG* 3.8 26.9 - - + -
72D ALA 2.9 10.6 + - - +
75D ALA* 1.3 86.0 - - + +
77D GLY* 1.3 64.3 + - - +
78D GLN* 3.3 8.0 + - - +
80D MET* 3.5 21.2 - - + +
119D LEU* 3.5 32.8 - - + -
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Residues in contact with GLY 77 (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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73D LYS* 2.7 27.5 + - - +
74D ILE 4.4 2.1 + - - -
75D ALA 3.8 0.6 - - - -
76D PHE* 1.3 76.7 - - - +
78D GLN* 1.3 64.9 + - - +
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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