Contacts of the helix formed by residues 62 - 77 (chain D) in PDB entry 3ECS
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 SER 62 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22D SER* 4.8 5.6 + - - -
60D ASP* 2.5 32.8 + - - +
61D SER* 1.3 74.1 - - - +
63D VAL* 1.3 67.0 + - - +
64D ALA* 3.4 19.2 + - - +
65D VAL* 3.4 16.3 + - - +
66D SER* 3.5 10.0 + - - -
198D GLU* 3.7 22.8 + - - +
250D PHE* 4.1 3.6 - - - -
255D ASP 5.2 5.2 - - - -
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Residues in contact with VAL 63 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61D SER 4.0 0.8 + - - -
62D SER* 1.3 72.3 + - - +
64D ALA* 1.3 50.1 + - - +
66D SER* 2.9 8.0 + - - -
67D SER* 2.7 36.0 + - - -
198D GLU* 3.9 28.5 - - + +
199D GLY* 4.5 2.7 - - - -
207D ILE* 3.8 34.8 - - + -
236D VAL* 4.1 29.4 - - + -
250D PHE* 3.5 45.3 - - + -
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Residues in contact with ALA 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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22D SER* 5.8 1.8 - - - -
23D ALA* 3.7 21.1 - - + +
62D SER* 3.2 10.8 + - - +
63D VAL* 1.3 76.1 - - - +
65D VAL* 1.3 57.0 + - + +
67D SER* 4.2 6.7 - - - +
68D GLY* 2.6 36.0 + - - -
198D GLU* 3.4 17.5 + - - +
233D PHE* 4.2 0.6 - - + +
234D LYS* 3.8 25.1 - - + +
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Residues in contact with VAL 65 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10D PHE* 4.4 3.6 - - + -
22D SER* 3.4 26.9 - - - +
23D ALA* 4.0 7.2 - - - +
26D ALA* 4.1 18.9 - - + +
54D GLU* 4.8 7.3 - - + +
57D CYS* 3.9 30.7 - - + +
58D GLY* 4.7 4.3 - - - +
60D ASP* 3.4 30.3 - - - +
62D SER* 3.4 13.6 + - - +
63D VAL 3.4 0.6 - - - -
64D ALA* 1.3 76.9 - - - +
66D SER* 1.3 62.4 + - - +
69D GLY* 3.1 20.3 + - - +
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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
----------------------------------------------------------
54D GLU* 4.0 5.5 - - - +
62D SER 3.5 8.4 + - - -
63D VAL 2.9 12.9 + - - -
65D VAL* 1.3 80.5 - - - +
67D SER* 1.3 62.9 + - - +
69D GLY* 3.9 0.2 - - - -
70D GLU* 3.0 30.7 + - - +
249D LYS* 5.3 1.7 + - - -
250D PHE* 4.0 23.3 - - - -
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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
----------------------------------------------------------
63D VAL* 2.7 21.3 + - - +
64D ALA* 3.8 2.2 - - - -
66D SER* 1.3 69.1 - - - +
68D GLY* 1.3 64.9 + - - +
70D GLU* 3.4 7.3 + - - +
71D LEU* 2.9 29.1 + - - +
233D PHE 3.0 21.5 - - - -
234D LYS* 3.9 6.3 + - - -
235D PHE 3.7 13.6 + - - -
236D VAL* 3.1 33.3 - - - +
304D TYR* 4.4 3.8 + - - -
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Residues in contact with GLY 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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23D ALA* 4.8 4.7 - - - -
27D ILE* 4.2 16.8 - - - -
64D ALA 2.6 20.5 + - - -
65D VAL 4.3 0.4 - - - -
67D SER* 1.3 74.7 - - - +
69D GLY* 1.3 54.7 + - - +
71D LEU* 3.2 2.6 + - - +
72D PHE* 2.8 30.5 + - - +
100D PHE* 4.2 3.1 - - - -
233D PHE* 3.4 20.8 + - - -
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Residues in contact with GLY 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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26D ALA* 6.1 0.8 - - - +
27D ILE* 4.5 3.7 - - - +
30D LEU* 4.0 13.5 - - - -
54D GLU* 2.9 26.7 - - - +
65D VAL 3.1 16.5 + - - -
68D GLY* 1.3 74.9 - - - +
70D GLU* 1.3 62.1 + - - +
72D PHE* 2.9 5.4 + - - +
73D LEU* 2.8 25.5 + - - +
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Residues in contact with GLU 70 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54D GLU* 2.8 11.9 + - - +
66D SER* 3.0 20.6 + - - +
67D SER* 3.6 6.9 - - - +
69D GLY* 1.3 73.6 - - - +
71D LEU* 1.3 58.4 + - - +
73D LEU* 3.2 6.5 + - - +
74D ARG* 2.9 35.8 + - + +
236D VAL* 6.5 0.7 - - - -
237D ARG* 3.4 36.8 + - - +
304D TYR* 3.6 15.5 + - + +
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Residues in contact with LEU 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 2.9 19.6 + - - +
68D GLY* 3.6 3.6 - - - +
70D GLU* 1.3 75.8 - - - +
72D PHE* 1.3 58.1 + - - +
74D ARG* 3.5 6.8 - - + +
75D PHE* 2.9 31.0 + - - +
100D PHE* 3.8 15.8 - - + -
232D SER 4.0 0.9 - - - +
233D PHE* 3.7 30.1 - - + +
235D PHE 4.6 0.4 - - - +
303D LEU* 3.5 33.2 - - + +
304D TYR* 3.8 50.9 - - + +
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Residues in contact with PHE 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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27D ILE* 4.4 15.5 - - + -
30D LEU* 3.9 31.0 - - + -
31D LEU* 4.1 26.7 - - + -
34D LEU* 5.4 1.3 - - + -
50D THR* 5.2 4.0 - - - -
68D GLY 2.8 13.7 + - - +
69D GLY* 3.3 9.0 - - - +
71D LEU* 1.3 73.2 - - - +
73D LEU* 1.3 83.5 + - + +
75D PHE* 3.2 1.4 + + - -
76D ILE* 2.8 54.4 + - + +
97D GLY* 3.6 29.2 - - - -
100D PHE* 3.7 34.5 - + + -
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Residues in contact with LEU 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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30D LEU* 4.8 1.1 - - + -
47D ALA 5.0 0.4 - - - +
50D THR* 3.7 41.3 - - + +
51D SER* 4.2 18.4 - - - +
54D GLU* 2.9 32.8 - - - +
69D GLY 2.8 11.7 + - - +
70D GLU* 3.7 7.4 - - - +
72D PHE* 1.3 87.9 - - + +
74D ARG* 1.3 57.5 + - - +
76D ILE* 3.3 8.0 - - + +
77D SER* 2.7 40.9 + - - +
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Residues in contact with ARG 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 GLU* 2.9 21.2 + - + +
71D LEU* 3.5 10.1 - - + +
72D PHE 3.0 0.2 - - - -
73D LEU* 1.3 80.8 - - - +
75D PHE* 1.3 62.4 + - - +
77D SER* 3.4 16.5 + - - +
237D ARG* 3.8 17.4 - - - +
304D TYR* 3.0 47.4 + - - +
305D LEU* 4.9 4.6 - - - +
307D ALA* 5.0 7.5 - - - +
241F LEU* 3.7 28.7 - - - +
242F ASN* 4.6 11.9 - - - +
245F ASP* 5.5 1.2 + - - -
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Residues in contact with PHE 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 LEU 2.9 16.6 + - - +
72D PHE 3.8 1.1 - - - +
74D ARG* 1.3 76.4 - - - +
76D ILE* 1.3 62.0 + - + +
77D SER 3.9 0.5 - - - +
96D ARG* 3.6 48.1 + - + -
97D GLY* 5.6 0.2 - - - -
99D LEU* 4.2 14.8 - - + -
100D PHE* 3.4 41.7 - + + -
103D ARG* 4.1 26.9 - - - -
306D ALA 4.4 17.9 - - - -
307D ALA* 4.8 16.6 - - + +
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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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34D LEU* 3.3 33.4 - - + -
50D THR* 6.0 2.7 - - + -
72D PHE* 2.8 42.8 + - + +
73D LEU* 3.3 22.7 - - + +
75D PHE* 1.3 79.6 - - + +
77D SER* 1.3 67.6 + - - +
93D MSE 3.2 46.9 - - + +
96D ARG* 2.9 23.9 + - - +
97D GLY* 4.0 8.1 - - - +
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Residues in contact with SER 77 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73D LEU* 2.7 28.1 + - - +
74D ARG* 3.4 14.6 + - - +
75D PHE 3.9 1.2 - - - +
76D ILE* 1.3 83.6 - - - +
78D LEU* 1.3 58.0 - - - +
93D MSE 4.1 9.6 - - - +
96D ARG* 2.6 20.3 + - - -
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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