Contacts of the helix formed by residues 67 - 81 (chain D) in PDB entry 3MGV
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 67 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62D LYS* 4.9 5.7 + - + +
65D PRO* 3.7 15.2 + - - +
66D ALA* 1.3 78.3 - - - +
68D PRO* 1.3 80.2 - - + +
69D GLU* 3.3 3.4 - - + +
70D ASP* 2.9 40.9 + - - +
71D VAL* 3.0 13.7 + - - +
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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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66D ALA 3.9 5.2 - - - +
67D GLU* 1.3 94.8 - - + +
69D GLU* 1.3 58.8 + - + +
71D VAL* 3.3 3.0 + - + -
72D ARG* 2.8 28.3 + - - +
106D ARG 6.0 0.2 - - - +
107D PRO* 5.0 6.7 - - + +
110D SER* 3.3 36.8 - - - +
112D ALA* 4.5 8.1 - - + -
113D VAL* 3.3 17.4 - - + +
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Residues in contact with GLU 69 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25C LYS* 3.8 18.0 + - - +
32C ARG* 2.5 43.7 + - - -
67D GLU* 3.3 3.4 - - + +
68D PRO* 1.3 79.6 - - + +
70D ASP* 1.3 61.3 + - - +
72D ARG* 3.5 7.6 + - - +
73D ASP* 3.1 35.6 + - - +
112D ALA* 3.5 15.6 - - - +
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Residues in contact with ASP 70 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52D TRP* 3.8 17.3 - - + -
55D TRP* 3.6 3.8 - - - -
61D ARG* 2.8 54.9 + - + +
62D LYS* 4.5 7.8 + - - +
67D GLU* 2.9 32.2 + - + +
69D GLU* 1.3 79.1 - - - +
71D VAL* 1.3 60.1 + - - +
73D ASP* 3.2 3.5 + - - +
74D TYR* 2.9 29.1 + - - +
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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
----------------------------------------------------------
52D TRP* 3.9 13.9 - - + -
66D ALA* 3.7 24.9 - - + -
67D GLU 3.0 15.3 + - - +
68D PRO 3.6 6.1 - - - +
70D ASP* 1.3 70.0 - - - +
72D ARG* 1.3 68.0 + - - +
74D TYR* 3.0 2.8 + - + +
75D LEU* 2.8 38.6 + - + +
92D LEU* 4.2 5.8 - - + -
95D LEU* 4.4 13.9 - - + -
107D PRO* 4.0 19.5 - - + -
113D VAL* 3.8 28.3 - - + -
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Residues in contact with ARG 72 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32C ARG* 3.5 49.4 - - - +
33C ASP* 2.8 39.4 + - - -
68D PRO 2.8 17.8 + - - +
69D GLU* 3.6 10.0 + - - +
70D ASP 3.2 0.2 - - - -
71D VAL* 1.3 77.3 - - - +
73D ASP* 1.3 70.4 + - - +
75D LEU* 3.2 2.8 + - - +
76D LEU* 3.0 45.0 + - + +
112D ALA* 3.6 21.5 - - - +
113D VAL* 4.1 2.0 - - - +
116D VAL* 3.7 23.2 - - + +
119D ARG* 3.4 13.3 - - - +
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Residues in contact with ASP 73 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55D TRP* 3.9 17.0 - - + -
61D ARG* 2.9 29.5 + - - +
69D GLU* 3.1 19.2 + - - +
70D ASP 3.5 8.1 - - - +
71D VAL 3.2 0.2 - - - -
72D ARG* 1.3 87.1 + - - +
74D TYR* 1.3 56.6 + - - +
76D LEU* 3.3 10.7 + - - +
77D TYR* 2.9 28.6 + - - +
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Residues in contact with TYR 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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48D VAL* 5.2 0.2 - - + -
51D SER* 2.8 21.0 + - - -
52D TRP* 3.4 49.2 + + + +
55D TRP* 3.7 34.4 - + + -
70D ASP 2.9 14.1 + - - +
71D VAL* 3.0 8.0 + - - +
73D ASP* 1.3 77.0 - - - +
75D LEU* 1.3 67.9 + - + +
77D TYR* 3.2 25.0 + + - +
78D LEU* 2.9 43.5 + - + +
91D HIS* 2.6 37.8 + - + -
95D LEU* 4.4 10.1 - - + -
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Residues in contact with LEU 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 VAL* 2.8 36.2 + - + +
72D ARG 3.7 3.8 - - - +
74D TYR* 1.3 82.0 - - + +
76D LEU* 1.3 57.5 + - - +
78D LEU* 3.2 16.4 + - + +
79D GLN 2.9 23.6 + - - -
88D ILE* 3.8 30.1 - - + +
92D LEU* 4.0 38.4 - - + +
95D LEU* 5.8 0.4 - - + -
113D VAL* 4.1 3.6 - - + -
116D VAL* 4.0 20.0 - - + -
117D MET* 4.6 6.1 - - - -
120D ILE* 3.6 22.8 - - + +
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Residues in contact with LEU 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 ARG* 3.0 53.2 + - + +
73D ASP* 3.5 13.0 - - - +
75D LEU* 1.3 75.2 - - - +
77D TYR* 1.3 57.4 + - - +
79D GLN* 3.4 26.6 + - - +
80D ALA* 3.0 28.6 + - - +
116D VAL* 3.9 18.8 - - + -
119D ARG* 5.3 11.0 - - - +
120D ILE* 4.2 5.6 - - + -
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Residues in contact with TYR 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 SER* 5.2 2.4 + - - -
55D TRP* 3.5 43.3 - + + +
73D ASP 2.9 13.0 + - - +
74D TYR* 3.3 28.7 - + - +
76D LEU* 1.3 74.0 - - - +
78D LEU* 1.3 81.0 + - + +
80D ALA* 3.3 7.5 + - + +
81D ARG* 3.0 57.8 + - + +
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Residues in contact with LEU 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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74D TYR* 2.9 43.7 + - + +
75D LEU* 3.6 17.7 - - + +
77D TYR* 1.3 86.2 - - + +
79D GLN* 1.3 63.0 + - - +
81D ARG* 3.3 39.1 + - - +
82D GLY 3.4 0.2 + - - -
83D LEU* 3.3 33.2 + - + +
88D ILE* 3.8 20.4 - - + -
91D HIS* 3.7 36.8 - - + -
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Residues in contact with GLN 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 LEU 2.9 13.3 + - - +
76D LEU* 3.5 30.1 - - - +
78D LEU* 1.3 76.6 - - - +
80D ALA* 1.3 58.2 + - - +
82D GLY* 2.8 22.5 + - - -
83D LEU 4.2 2.1 + - - +
88D ILE* 3.7 16.5 - - + +
120D ILE* 3.7 19.3 - - + +
123D GLU* 3.0 32.2 + - - +
124D ASN* 3.0 32.0 + - - +
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Residues in contact with ALA 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 LEU 3.0 17.5 + - - +
77D TYR* 3.3 7.4 + - - +
79D GLN* 1.3 72.2 - - - +
81D ARG* 1.3 60.9 + - + +
82D GLY* 3.1 6.1 + - - -
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Residues in contact with ARG 81 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51D SER* 4.5 8.5 + - - -
77D TYR* 3.0 56.5 + - + +
78D LEU* 3.5 31.2 - - - +
79D GLN 3.2 0.2 - - - -
80D ALA* 1.3 75.2 - - + +
82D GLY* 1.3 60.8 + - - +
83D LEU* 3.6 22.8 + - + +
91D HIS* 5.7 0.4 - - - -
12I A 2.8 35.4 + - - -
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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