Contacts of the helix formed by residues 64 - 78 (chain D) in PDB entry 4GG6
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 GLN 64 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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60D TYR* 3.1 61.3 + - + +
61D TRP* 3.1 22.8 + - - +
62D ASN 3.0 4.5 - - - -
63D SER* 1.3 82.2 - - - +
65D LYS* 1.3 65.9 + - - +
66D GLU* 3.2 21.2 + - - +
67D VAL* 3.2 29.9 + - + +
68D LEU* 3.2 8.1 + - - +
108F VAL* 4.8 11.3 - - - +
114F TYR* 5.5 3.2 - - - -
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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
----------------------------------------------------------
62D ASN 4.6 1.7 + - - -
63D SER 3.9 3.8 + - - -
64D GLN* 1.3 71.2 - - - +
66D GLU* 1.3 67.4 + - + +
68D LEU* 3.5 7.9 + - - +
69D GLU* 3.2 34.1 + - + +
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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 GLN* 3.5 28.1 + - - +
65D LYS* 1.3 86.5 + - + +
67D VAL* 1.3 66.1 + - + +
69D GLU* 3.6 3.5 + - - +
70D ARG* 3.2 26.1 + - - +
55E HIS* 5.0 11.4 + - + -
113F THR* 3.8 21.7 - - - +
114F TYR* 5.0 14.8 - - + -
115F GLU* 5.7 7.7 - - + +
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Residues in contact with VAL 67 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47D TYR* 4.3 19.3 - - + +
61D TRP* 4.0 21.1 - - + +
64D GLN* 3.2 40.9 + - + +
66D GLU* 1.3 75.9 - - - +
68D LEU* 1.3 59.9 + - - +
70D ARG* 3.3 9.4 - - + +
71D THR* 2.7 35.0 + - - +
114F TYR* 3.8 32.5 - - + +
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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
----------------------------------------------------------
40D PHE* 4.1 4.9 - - + -
45D GLY 4.0 6.1 - - - +
46D VAL* 4.0 24.2 - - + -
47D TYR* 3.9 16.2 - - + -
61D TRP 4.3 5.8 + - - +
62D ASN* 3.6 36.6 - - + +
64D GLN 3.2 12.2 + - - +
65D LYS* 3.9 10.5 - - - +
66D GLU 3.3 0.2 - - - -
67D VAL* 1.3 73.2 - - - +
69D GLU* 1.3 55.5 + - + +
70D ARG 3.1 1.6 - - - -
71D THR* 2.9 6.3 + - - -
72D ARG* 2.7 67.5 + - - +
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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
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65D LYS* 3.2 22.2 + - + +
66D GLU* 4.3 3.8 - - - +
68D LEU* 1.3 74.6 - - + +
70D ARG* 1.3 56.6 + - - +
72D ARG* 3.1 38.1 + - - +
73D ALA* 3.1 29.1 + - - +
38E TYR* 4.0 2.8 + - - -
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Residues in contact with ARG 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 3.2 13.6 + - - +
67D VAL* 3.3 18.2 - - - +
68D LEU 3.1 0.6 - - - -
69D GLU* 1.3 76.2 - - - +
71D THR* 1.3 66.8 + - - +
72D ARG 3.4 0.2 - - - -
73D ALA* 3.7 1.9 + - - +
74D GLU* 3.0 60.6 + - - +
77D THR* 5.2 0.2 + - - -
38E TYR* 3.9 10.9 + - + -
109E GLY* 2.7 33.1 + - - -
110E ARG* 4.0 11.1 - - - +
111F SER* 5.3 1.7 + - - -
113F THR* 2.7 39.3 + - + +
114F TYR* 3.6 27.9 - - - -
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Residues in contact with THR 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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26D LEU* 3.8 9.3 - - + +
28D THR* 4.4 10.3 - - + +
30D TYR* 5.5 0.2 - - - +
40D PHE* 3.6 33.6 - - + -
47D TYR* 2.7 32.1 + - + +
67D VAL* 2.7 22.2 + - - +
68D LEU 2.9 3.9 + - - -
70D ARG* 1.3 80.9 + - - +
72D ARG* 1.3 66.4 + - - +
74D GLU* 3.3 33.0 + - - +
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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
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26D LEU* 4.5 1.0 - - - +
40D PHE* 3.6 21.5 - - + -
42D SER* 5.7 2.2 - - - -
45D GLY* 2.8 28.5 + - - +
46D VAL* 3.8 16.2 - - - +
68D LEU* 2.7 38.0 + - - +
69D GLU* 3.1 37.0 + - - +
71D THR* 1.3 77.9 - - - +
73D ALA* 1.3 59.8 + - - +
74D GLU 3.3 0.9 + - - -
75D LEU* 3.4 21.0 + - - +
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Residues in contact with ALA 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 GLU 3.1 20.4 + - - +
70D ARG 4.1 2.0 - - - +
71D THR 3.3 0.2 - - - -
72D ARG* 1.3 71.1 - - - +
74D GLU* 1.3 56.3 + - - +
75D LEU 2.9 5.8 - - - -
76D ASP* 2.8 24.1 + - - +
77D THR* 2.9 16.3 + - + +
38E TYR* 3.4 20.4 - - - +
57E LEU* 3.8 20.2 - - + -
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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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11D PHE* 6.1 0.5 - - - -
26D LEU* 3.6 10.4 - - + +
28D THR* 4.8 10.3 - - + +
70D ARG* 3.0 47.5 + - - +
71D THR* 3.3 31.6 + - - +
72D ARG 3.2 1.0 - - - -
73D ALA* 1.3 77.0 - - - +
75D LEU* 1.3 56.0 + - - +
76D ASP 3.2 0.2 - - - -
77D THR* 3.2 16.8 - - - +
78D VAL* 2.8 46.5 + - + +
79D CYS 3.2 2.6 + - - -
110E ARG* 5.8 2.1 - - - +
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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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24D VAL* 3.8 34.3 - - + +
25D ARG* 4.1 3.6 - - - -
26D LEU* 3.3 35.3 - - + +
42D SER* 4.2 17.0 - - - +
72D ARG 3.4 13.9 + - - +
73D ALA* 2.9 0.4 - - - -
74D GLU* 1.3 78.6 - - - +
76D ASP* 1.3 57.2 + - - +
79D CYS* 3.3 11.1 - - - +
80D ARG* 2.9 51.9 + - - +
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Residues in contact with ASP 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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73D ALA* 2.8 10.3 + - - +
75D LEU* 1.3 78.6 - - - +
77D THR* 1.3 63.7 + - + +
78D VAL 3.2 0.4 - - - -
80D ARG* 2.8 41.5 + - - +
81D HIS* 3.1 30.3 + - - +
30E GLY 5.3 2.2 - - - +
57E LEU* 5.1 11.0 - - + +
58E THR* 5.7 1.6 + - - +
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Residues in contact with THR 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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70D ARG 5.2 0.2 + - - -
73D ALA* 2.9 15.5 + - + +
74D GLU* 3.2 26.2 - - - +
76D ASP* 1.3 75.9 - - + +
78D VAL* 1.3 62.8 + - - +
81D HIS* 3.6 14.4 - - - +
82D ASN* 5.0 0.3 - - - +
30E GLY 4.0 19.7 - - - +
36E THR* 4.0 28.8 - - + +
38E TYR* 4.7 9.4 - - + -
57E LEU* 4.1 26.0 - - + -
109E GLY* 6.6 0.2 - - - -
110E ARG* 5.8 0.9 - - - -
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Residues in contact with VAL 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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9C TYR* 3.8 35.7 - - + +
13D GLY 5.9 0.4 - - - +
15D CYS* 4.5 5.2 - - - -
26D LEU* 6.2 0.2 - - + -
74D GLU* 2.8 41.3 + - + +
77D THR* 1.3 85.9 - - - +
79D CYS* 1.3 56.6 + - - +
80D ARG 3.7 0.2 - - - -
81D HIS* 3.3 1.6 + - - +
82D ASN* 2.8 46.5 + - - +
110E ARG* 6.3 3.1 - - - -
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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