Contacts of the helix formed by residues 65 - 80 (chain D) in PDB entry 3COG
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 ASN 65 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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42D SER 4.6 5.1 - - - +
44D SER 5.3 0.2 - - - +
47D PHE* 4.4 4.9 - - + -
58D PHE* 3.4 8.0 - - - -
61D SER* 3.0 40.4 + - - +
64D GLY* 1.3 74.6 - - - +
66D PRO* 1.3 76.8 - - + +
67D THR 3.7 3.3 + - - -
68D ARG* 3.0 48.3 + - - +
69D ASN* 3.0 26.8 + - - +
247D PRO 5.2 3.2 + - - -
249D PRO* 4.0 20.8 - - - +
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Residues in contact with PRO 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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34B SER* 3.7 20.0 - - - -
32D TRP* 4.1 23.6 - - + -
40D PRO 5.5 0.9 - - - +
42D SER* 4.0 22.9 - - - +
47D PHE* 4.0 15.7 - - + -
58D PHE* 3.6 29.6 - - + -
65D ASN* 1.3 88.8 - - + +
67D THR* 1.3 64.0 + - - +
69D ASN* 3.3 2.7 + - + +
70D CYS* 3.1 30.9 + - - -
604D GOL 5.2 0.9 - - - +
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Residues in contact with THR 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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32D TRP* 5.8 0.2 - - - -
39D PRO* 5.6 4.5 - - + +
40D PRO 2.8 27.8 + - - +
41D ILE* 4.5 2.2 - - - -
42D SER* 3.0 20.7 + - - -
65D ASN* 3.5 1.8 + - - -
66D PRO* 1.3 75.3 - - - +
68D ARG* 1.3 62.7 + - - +
70D CYS* 3.5 8.2 + - + +
71D LEU* 3.3 20.8 + - - +
249D PRO* 3.3 33.2 - - - +
252D CYS* 4.1 1.1 - - + +
253D TYR* 3.7 27.8 - - + +
256D ASN* 5.0 1.1 - - + +
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Residues in contact with ARG 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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61D SER 3.7 8.7 + - - -
62D ARG* 3.0 21.6 + - - +
63D SER 3.0 30.5 + - - -
64D GLY* 3.5 4.7 - - - -
65D ASN* 3.0 32.8 + - - +
67D THR* 1.3 73.8 - - - +
69D ASN* 1.3 65.7 + - - +
71D LEU* 3.3 2.5 + - - +
72D GLU* 2.9 57.7 + - - +
86D ALA* 4.0 5.6 - - + -
237D ARG* 5.0 1.8 - - - +
240D GLN* 3.3 24.8 + - - +
246D VAL* 3.4 22.2 - - - +
247D PRO* 3.9 22.4 + - - -
252D CYS* 3.7 25.4 - - - +
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Residues in contact with ASN 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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58D PHE* 3.5 23.7 - - + -
64D GLY* 3.9 8.9 - - - -
65D ASN 3.0 32.0 + - - +
66D PRO* 3.8 4.7 - - + +
68D ARG* 1.3 83.0 + - - +
70D CYS* 1.3 57.1 + - - +
72D GLU* 3.3 17.0 + - - +
73D LYS* 3.0 37.1 + - + +
237D ARG* 5.6 0.5 + - - -
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Residues in contact with CYS 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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26D GLY* 3.2 30.4 - - - +
27D GLN* 3.9 10.3 + - - +
31D GLN* 3.6 17.3 - - - -
32D TRP* 3.6 21.8 - - - -
39D PRO* 4.3 9.2 - - + -
66D PRO 3.1 22.6 + - - -
67D THR* 3.6 9.2 - - + +
68D ARG 3.2 0.2 - - - -
69D ASN* 1.3 75.2 - - - +
71D LEU* 1.3 65.2 + - - +
73D LYS* 3.4 6.7 + - - +
74D ALA* 3.1 22.7 + - - +
256D ASN* 3.8 3.8 - - - +
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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 THR 3.3 9.6 + - - +
68D ARG 3.3 7.4 + - - +
70D CYS* 1.3 77.7 - - - +
72D GLU* 1.3 64.2 + - - +
74D ALA* 3.1 3.0 + - - +
75D VAL* 2.9 35.7 + - + +
86D ALA* 4.4 4.9 - - + -
222D MET* 3.7 29.4 - - - -
224D LEU* 4.2 9.4 - - + -
252D CYS* 3.8 30.5 - - + +
255D CYS* 4.2 5.6 - - + -
256D ASN* 3.3 29.9 + - + +
259D LEU* 3.7 27.4 - - + -
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Residues in contact with GLU 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 ARG* 2.9 31.9 + - - +
69D ASN* 3.7 18.5 - - - +
71D LEU* 1.3 77.2 - - - +
73D LYS* 1.3 62.6 + - - +
76D ALA* 3.0 21.2 + - - +
84D CYS* 3.2 40.9 - - - +
85D LEU 4.2 0.2 - - - -
86D ALA* 2.8 37.0 + - + +
224D LEU* 5.6 0.2 - - + -
237D ARG* 3.0 19.7 + - - -
240D GLN* 2.9 18.5 + - - -
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Residues in contact with LYS 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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25D VAL* 3.3 18.9 - - + +
26D GLY* 4.1 19.2 - - - +
31D GLN* 4.3 17.6 + - - +
69D ASN* 3.0 23.3 + - + +
70D CYS* 3.6 9.4 - - - +
71D LEU 3.3 0.2 - - - -
72D GLU* 1.3 74.5 - - - +
74D ALA* 1.3 63.7 + - - +
76D ALA* 3.5 7.0 + - - +
77D ALA* 3.2 18.0 + - - +
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Residues in contact with ALA 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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21D GLN 5.1 1.5 - - - +
22D ALA 5.1 7.0 - - - +
25D VAL* 3.4 30.4 - - + +
70D CYS 3.1 8.7 + - - +
71D LEU 3.1 8.3 + - - +
73D LYS* 1.3 78.4 - - - +
75D VAL* 1.3 61.3 + - - +
77D ALA* 3.2 6.1 + - - +
78D LEU* 3.1 29.8 + - + +
256D ASN* 4.2 19.5 - - - +
259D LEU* 4.7 7.0 - - + -
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Residues in contact with VAL 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 29.0 + - + +
74D ALA* 1.3 71.5 - - - +
76D ALA* 1.3 65.5 + - - +
78D LEU* 3.0 8.4 + - + +
79D ASP* 2.9 37.6 + - - +
84D CYS* 3.8 21.1 - - - -
208D TYR* 4.9 0.4 - - + -
214D MET* 3.9 18.8 - - + -
224D LEU* 3.9 24.2 - - + -
226D SER* 3.9 0.4 - - - +
259D LEU* 3.5 25.4 - - + -
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Residues in contact with ALA 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 GLU 3.0 17.7 + - - +
73D LYS* 3.6 7.9 - - - +
75D VAL* 1.3 75.4 - - - +
77D ALA* 1.3 60.3 + - - +
79D ASP* 3.2 2.6 + - - -
80D GLY 3.0 3.8 + - - -
81D ALA* 2.7 45.7 + - - +
82D LYS 4.1 3.1 - - - +
83D TYR* 3.7 26.2 - - - +
84D CYS* 3.7 5.7 - - - +
226D SER* 4.1 6.1 - - - -
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Residues in contact with ALA 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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21D GLN* 3.8 21.5 - - + +
25D VAL* 3.9 26.9 - - + -
73D LYS 3.2 10.6 + - - +
74D ALA 3.2 8.9 + - - +
76D ALA* 1.3 78.8 - - - +
78D LEU* 1.3 64.2 - - + +
80D GLY* 3.1 13.0 + - - -
81D ALA 4.3 3.5 + - - +
197D ARG* 3.7 8.0 + - - -
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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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18D PHE* 3.6 57.4 - - + +
21D GLN* 4.2 7.9 - - + +
22D ALA* 3.7 26.9 - - + +
74D ALA* 3.1 13.6 + - + +
75D VAL* 3.0 11.2 + - + +
77D ALA* 1.3 78.8 - - - +
79D ASP* 1.3 56.5 + - - +
193D PRO* 3.3 21.3 - - + +
197D ARG* 3.0 25.8 + - - +
214D MET* 5.6 1.1 - - + -
259D LEU* 4.0 28.5 - - + +
262D LEU* 4.5 6.1 - - + -
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Residues in contact with ASP 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 VAL* 2.9 19.5 + - - +
76D ALA 3.2 4.9 + - - +
78D LEU* 1.3 75.5 - - - +
80D GLY* 1.3 60.4 + - - +
81D ALA* 4.1 2.7 - - + -
188D ASN* 4.5 0.5 + - - -
193D PRO* 3.8 5.7 - - - +
196D GLN 5.1 0.3 - - - +
197D ARG* 3.9 18.9 - - - +
198D PRO* 4.8 3.6 - - - +
199D LEU* 4.1 17.7 - - + +
200D ALA 5.2 0.7 + - - -
206D SER* 3.0 14.5 + - - -
208D TYR* 2.5 40.9 + - - -
226D SER* 2.7 37.3 + - - +
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Residues in contact with GLY 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 ALA 3.0 3.5 + - - -
77D ALA* 3.1 13.2 + - - -
78D LEU 3.3 1.4 + - - -
79D ASP* 1.3 78.3 - - - +
81D ALA* 1.3 58.2 + - - +
197D ARG* 4.0 12.3 - - - +
199D LEU* 4.8 2.1 - - - +
228D ASN* 3.9 10.7 + - - +
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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