Contacts of the helix formed by residues 58 - 76 (chain D) in PDB entry 2JIF
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 THR 58 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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57D PHE* 1.3 77.5 - - - +
59D ASP* 1.3 63.8 + - - +
60D GLU* 3.5 7.9 + - - +
61D GLU* 2.9 42.0 + - - +
62D MET* 3.0 21.5 + - - +
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Residues in contact with ASP 59 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57D PHE 5.1 0.2 - - - +
58D THR* 1.3 73.2 - - - +
60D GLU* 1.3 58.7 + - - +
62D MET* 3.1 26.4 + - - +
63D MET* 2.9 42.1 + - + +
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Residues in contact with GLU 60 (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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58D THR* 3.3 7.8 + - - +
59D ASP* 1.3 76.9 - - - +
61D GLU* 1.3 58.8 + - + +
63D MET* 3.3 18.2 + - + +
64D ILE* 2.9 46.9 + - + +
114D THR* 3.9 19.2 - - - +
115D GLY 4.4 3.5 - - - +
116D ALA* 3.5 34.0 - - - +
117D SER* 4.3 3.5 + - - -
120D SER* 4.8 1.1 + - - +
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Residues in contact with GLU 61 (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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56D THR 4.9 0.3 - - - +
57D PHE* 3.5 16.8 - - + +
58D THR* 2.9 44.3 + - - +
60D GLU* 1.3 78.3 - - + +
62D MET* 1.3 56.8 + - - +
64D ILE* 3.4 2.1 + - - +
65D LYS* 3.0 30.0 + - - +
117D SER* 2.7 23.9 + - - +
119D LEU* 3.5 28.5 - - - +
120D SER* 3.2 27.8 - - - +
123D LEU* 4.0 15.3 - - + +
355D ARG* 5.0 2.6 + - - -
358D GLU* 4.2 2.8 - - - +
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Residues in contact with MET 62 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57D PHE* 3.8 31.9 - - + +
58D THR 3.0 14.6 + - - +
59D ASP* 3.1 39.7 - - - +
61D GLU* 1.3 75.6 - - - +
63D MET* 1.3 63.7 + - + +
65D LYS* 3.5 7.5 + - - +
66D SER* 3.1 26.4 + - - -
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Residues in contact with MET 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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59D ASP* 2.9 22.6 + - + +
60D GLU* 3.7 26.5 - - + +
62D MET* 1.3 77.8 - - + +
64D ILE* 1.3 58.9 + - + +
66D SER* 3.4 6.8 + - - -
67D SER* 3.0 33.4 + - - +
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Residues in contact with ILE 64 (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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60D GLU* 2.9 34.5 + - + +
61D GLU* 3.9 4.0 - - - +
63D MET* 1.3 73.7 - - + +
65D LYS* 1.3 67.0 + - - +
67D SER* 3.3 6.0 + - - -
68D VAL* 3.0 32.6 + - + +
102D LEU* 4.8 5.6 - - + -
105D ILE* 5.0 3.8 - - + -
114D THR* 4.5 12.3 - - + -
116D ALA* 3.6 31.2 - - + -
120D SER* 3.8 13.0 - - - +
123D LEU* 6.3 0.4 - - + -
124D VAL* 3.5 30.3 - - + -
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Residues in contact with LYS 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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57D PHE* 4.2 29.8 - - + -
61D GLU 3.0 17.9 + - - +
62D MET* 3.6 7.4 - - - +
64D ILE* 1.3 77.5 - - - +
66D SER* 1.3 57.3 + - - +
68D VAL* 3.4 3.5 + - - -
69D LYS* 3.0 29.3 + - + +
123D LEU* 4.7 25.7 - - + +
126D GLU* 5.9 2.6 + - - -
127D GLU* 3.5 34.1 - - + +
130D LYS* 4.6 9.0 - - - +
351D TYR* 5.1 5.6 + - - -
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Residues in contact with SER 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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62D MET 3.1 15.3 + - - -
63D MET* 3.6 7.2 - - - -
64D ILE 3.2 0.2 - - - -
65D LYS* 1.3 76.7 - - - +
67D SER* 1.3 66.4 + - - +
69D LYS* 3.4 9.9 + - - +
70D LYS* 3.2 22.2 + - - +
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Residues in contact with SER 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 MET* 3.0 18.4 + - - +
64D ILE* 3.3 7.6 + - - -
66D SER* 1.3 75.1 - - - +
68D VAL* 1.3 59.7 + - - +
70D LYS* 3.4 8.4 + - - +
71D PHE* 3.0 29.6 + - - +
100D GLN* 4.3 14.9 + - - -
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Residues in contact with VAL 68 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64D ILE* 3.0 17.9 + - + +
65D LYS* 3.8 4.3 - - - +
67D SER* 1.3 74.8 - - - +
69D LYS* 1.3 59.4 + - - +
71D PHE* 3.7 5.7 - - + +
72D ALA* 2.8 30.5 + - - +
100D GLN* 6.2 0.4 - - - +
102D LEU* 3.6 36.1 - - + -
124D VAL* 3.9 16.6 - - + +
127D GLU* 3.8 23.8 - - + -
128D LEU* 3.8 33.7 - - + +
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Residues in contact with LYS 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 LYS* 3.0 14.9 + - + +
66D SER* 3.6 13.5 - - - +
67D SER 3.4 0.2 - - - -
68D VAL* 1.3 75.8 - - - +
70D LYS* 1.3 57.6 + - - +
72D ALA* 3.9 4.0 - - - +
73D GLN* 3.0 59.4 + - - +
127D GLU* 3.6 27.0 - - - +
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Residues in contact with LYS 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 SER 3.2 9.4 + - - +
67D SER* 3.6 10.3 - - - +
69D LYS* 1.3 77.2 - - - +
71D PHE* 1.3 60.1 + - - +
73D GLN* 3.4 4.4 + - - -
74D GLU* 2.9 74.5 + - + +
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Residues in contact with PHE 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 SER 3.0 17.0 + - - +
68D VAL* 3.7 4.5 - - - +
70D LYS* 1.3 76.9 - - - +
72D ALA* 1.3 56.6 + - - +
74D GLU* 4.9 2.0 - - - -
75D GLN* 2.7 70.0 + - + +
76D ILE* 3.7 26.4 + - + -
92D SER 5.5 0.4 - - - -
93D VAL* 4.2 8.7 - - - -
96D GLY* 3.7 36.1 - - - -
97D LEU* 3.7 21.5 - - + -
99D GLN* 5.1 2.9 - - - -
100D GLN* 3.7 27.1 - - + +
102D LEU* 4.2 15.5 - - + -
128D LEU* 4.4 4.0 - - + -
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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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68D VAL 2.8 21.8 + - - +
69D LYS* 3.9 4.3 - - - +
71D PHE* 1.3 72.4 - - - +
73D GLN* 1.3 58.2 + - - +
76D ILE* 3.0 28.5 + - + +
77D ALA* 2.9 27.7 + - - +
127D GLU 4.6 8.3 - - - +
128D LEU* 4.5 9.0 - - + -
131D VAL* 3.7 28.0 - - + +
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Residues in contact with GLN 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 LYS* 3.0 50.6 + - - +
70D LYS* 4.0 5.1 - - - +
72D ALA* 1.3 77.1 - - - +
74D GLU* 1.3 64.0 + - + +
77D ALA* 3.6 22.1 - - + +
78D PRO* 3.8 5.2 - - - +
127D GLU* 5.6 0.2 + - - -
131D VAL* 4.7 12.5 - - + +
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Residues in contact with GLU 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 LYS* 2.9 64.3 + - + +
71D PHE* 4.2 2.2 - - - +
73D GLN* 1.3 80.7 - - + +
75D GLN* 1.3 77.5 + - + +
76D ILE 3.7 0.2 - - - -
78D PRO* 3.7 15.8 - - - +
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Residues in contact with GLN 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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71D PHE* 2.7 52.6 + - + +
74D GLU* 1.3 91.5 + - + +
76D ILE* 1.3 59.1 + - - +
78D PRO* 4.2 2.5 - - - -
79D LEU* 3.6 22.0 - - - +
92D SER* 5.2 10.5 + - - +
93D VAL* 4.0 6.0 - - + +
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Residues in contact with ILE 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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71D PHE* 3.7 21.8 - - + -
72D ALA* 3.0 20.8 + - + +
75D GLN* 1.3 81.1 - - - +
77D ALA* 1.3 57.7 + - - +
78D PRO* 3.3 3.4 - - - -
79D LEU* 2.8 28.9 + - - +
80D VAL* 3.3 17.6 + - + -
83D MET* 4.4 6.5 - - + -
93D VAL* 4.3 13.0 - - + -
128D LEU* 3.6 32.3 - - + +
131D VAL* 3.8 15.7 - - + -
132D ASP* 4.0 2.9 - - + -
135D VAL* 3.7 35.7 - - + -
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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