Contacts of the helix formed by residues 67 - 81 (chain D) in PDB entry 3C6Q
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 67 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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43D ILE* 3.8 28.2 - - + +
65D PRO* 4.1 1.8 - - - -
66D SER* 1.3 80.5 - - - +
68D PRO* 1.3 68.9 - - - +
69D THR* 2.7 21.9 + - - -
70D ALA* 2.6 35.4 + - - +
71D VAL* 2.9 27.2 + - - +
134D THR* 4.0 20.6 - - - +
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Residues in contact with PRO 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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65D PRO* 4.1 5.6 - - + +
66D SER 4.2 1.1 - - - +
67D ASP* 1.3 88.9 - - - +
69D THR* 1.3 66.6 + - - +
71D VAL* 3.2 8.3 - - - +
72D ILE* 3.3 6.4 - - - +
91D ASP 3.8 11.9 - - - +
92D SER* 2.8 35.0 + - - -
93D PRO* 5.0 1.8 - - + -
134D THR* 3.0 28.5 - - - +
135D ALA* 4.5 0.9 - - - +
136D MET* 3.4 29.6 - - + +
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Residues in contact with THR 69 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67D ASP* 2.7 14.9 + - - -
68D PRO* 1.3 76.7 - - - +
70D ALA* 1.3 65.0 + - - +
72D ILE* 3.1 32.8 + - + +
73D PRO* 3.9 3.6 - - - +
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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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43D ILE* 3.4 31.4 - - + -
47D LEU* 4.2 16.2 - - + +
67D ASP* 2.6 21.4 + - - +
69D THR* 1.3 73.0 - - - +
71D VAL* 1.3 60.7 + - - +
73D PRO* 3.4 12.6 - - - +
74D THR* 4.4 2.8 + - - -
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Residues in contact with VAL 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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43D ILE* 3.4 19.7 - - + -
47D LEU* 4.1 13.5 - - + -
50D LEU* 5.7 1.1 - - + -
63D ILE* 4.8 9.2 - - + -
65D PRO* 3.6 19.5 - - + -
67D ASP 2.9 17.3 - - - +
68D PRO 3.2 16.2 - - - +
70D ALA* 1.3 75.6 - - - +
72D ILE* 1.3 73.3 + - - +
73D PRO* 3.4 0.7 - - - -
74D THR* 3.2 7.7 + - - -
75D ILE* 3.1 35.3 + - + +
92D SER* 3.6 20.9 - - - +
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Residues in contact with ILE 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 PRO 3.3 15.7 - - - +
69D THR* 3.1 26.0 + - + +
71D VAL* 1.3 76.4 - - - +
73D PRO* 1.3 74.1 - - + +
75D ILE* 2.9 15.6 + - - +
76D LYS* 2.9 15.2 + - + +
92D SER* 3.8 7.4 - - - +
94D ASP* 4.0 37.5 - - + +
95D SER* 4.1 13.0 - - - +
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Residues in contact with PRO 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 THR 3.9 3.8 - - - +
70D ALA 3.4 16.2 - - - +
71D VAL 3.5 0.7 - - - -
72D ILE* 1.3 97.4 - - + +
74D THR* 1.3 62.9 + - - +
75D ILE 3.1 1.0 + - - -
76D LYS* 3.1 9.8 + - + +
77D LYS* 3.1 23.2 + - - +
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Residues in contact with THR 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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47D LEU* 3.8 24.8 - - + +
50D LEU* 3.7 34.7 - - + +
51D GLU* 3.6 34.1 + - + +
54D ILE* 3.7 12.3 - - + +
70D ALA 4.4 3.1 + - - -
71D VAL* 3.2 8.5 + - - -
73D PRO* 1.3 80.1 - - - +
75D ILE* 1.3 60.4 + - - +
77D LYS* 3.8 5.8 + - + +
78D ALA* 3.4 15.8 + - - +
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Residues in contact with ILE 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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50D LEU* 4.5 12.8 - - + -
63D ILE* 4.1 15.7 - - + -
65D PRO* 5.0 2.5 - - + -
71D VAL* 3.1 28.2 + - + +
72D ILE 2.9 8.6 + - - +
74D THR* 1.3 76.7 - - - +
76D LYS* 1.3 66.1 + - - +
77D LYS 3.1 2.0 + - - -
78D ALA* 3.2 6.5 + - - +
79D LEU* 3.0 32.3 + - + +
85D VAL* 3.8 33.7 - - + -
87D THR* 5.3 0.9 - - + -
92D SER* 5.1 0.2 - - - -
95D SER* 3.8 39.5 - - - +
97D ARG* 4.5 2.0 - - + +
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Residues in contact with LYS 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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72D ILE* 2.9 15.9 + - + +
73D PRO* 3.7 11.0 - - + +
75D ILE* 1.3 77.2 - - - +
77D LYS* 1.3 56.5 + - - +
79D LEU* 3.5 13.7 - - + +
80D GLU* 3.0 59.4 + - - +
95D SER 4.3 8.5 + - - +
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Residues in contact with LYS 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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51D GLU* 3.3 29.2 + - - +
54D ILE* 4.4 17.5 - - + -
73D PRO 3.1 14.5 + - - +
74D THR* 3.9 6.7 - - - +
75D ILE 3.1 0.8 - - - -
76D LYS* 1.3 75.1 - - - +
78D ALA* 1.3 66.1 + - - +
80D GLU* 2.9 30.9 + - - +
81D MET* 2.9 31.3 + - + +
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Residues in contact with ALA 78 (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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50D LEU* 5.9 1.3 - - + -
54D ILE* 3.7 28.4 - - + +
61D ILE* 4.3 10.8 - - + -
74D THR 3.4 7.2 + - - +
75D ILE* 3.2 8.6 + - - +
77D LYS* 1.3 77.0 - - - +
79D LEU* 1.3 61.9 + - - +
81D MET* 3.1 14.3 + - - +
82D GLY 3.3 0.2 + - - -
83D ILE* 2.9 31.0 + - + +
85D VAL* 4.1 18.6 - - + -
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Residues in contact with LEU 79 (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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75D ILE* 3.0 26.9 + - + +
76D LYS* 3.5 16.6 - - + +
78D ALA* 1.3 76.7 - - - +
80D GLU* 1.3 52.6 + - - +
82D GLY* 2.7 25.8 + - - -
83D ILE 3.4 19.0 + - - +
85D VAL* 3.7 22.0 - - + +
95D SER 4.3 0.2 - - - +
96D GLY* 3.4 35.4 - - - +
98D TYR* 4.0 28.3 + - + +
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Residues in contact with GLU 80 (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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76D LYS* 3.0 47.5 + - - +
77D LYS* 2.9 33.8 + - + +
79D LEU* 1.3 65.9 - - - +
81D MET* 1.3 60.6 + - + +
82D GLY* 2.8 11.6 + - - -
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Residues in contact with MET 81 (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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54D ILE* 4.1 23.6 - - + +
77D LYS* 2.9 30.5 + - + +
78D ALA* 3.1 11.8 + - - +
80D GLU* 1.3 75.0 - - - +
82D GLY* 1.3 60.4 + - - +
83D ILE* 4.0 15.6 - - + +
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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