Contacts of the helix formed by residues 27 - 43 (chain A) in PDB entry 2COP
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 27 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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25A VAL 3.9 3.7 + - - -
26A ALA* 1.3 73.3 - - - +
28A ARG* 1.3 60.4 + - - +
29A GLU* 3.1 10.5 - - - -
30A GLN* 2.6 41.5 + - - +
31A LEU* 2.9 12.5 + - - +
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Residues in contact with ARG 28 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26A ALA 4.0 0.4 + - - -
27A SER* 1.3 73.4 - - - +
29A GLU* 1.3 71.6 + - - +
31A LEU* 3.1 22.8 + - - +
32A LEU* 3.4 6.9 + - - +
60A GLN* 5.5 6.0 + - - +
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Residues in contact with GLU 29 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27A SER* 3.1 8.4 - - - -
28A ARG* 1.3 85.7 + - - +
30A GLN* 1.3 60.5 + - + +
32A LEU* 3.1 8.4 + - - +
33A TYR* 2.9 29.5 + - - +
60A GLN* 5.9 3.6 - - - +
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Residues in contact with GLN 30 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26A ALA* 3.9 13.0 - - + -
27A SER* 2.6 41.5 + - - +
29A GLU* 1.3 74.2 - - + +
31A LEU* 1.3 58.1 + - - +
32A LEU 3.4 0.7 + - - -
33A TYR* 3.4 14.0 + - - +
34A LEU* 3.3 29.1 + - + +
83A VAL* 3.3 31.6 - - + +
86A LYS* 6.0 1.2 - - - +
87A LEU* 3.5 19.0 - - + +
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Residues in contact with LEU 31 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19A LEU* 3.8 14.3 - - + +
23A ILE* 3.5 38.6 - - + +
26A ALA* 3.2 31.2 - - + +
27A SER 2.9 30.5 + - - +
28A ARG* 3.3 11.4 - - - +
30A GLN* 1.3 78.2 - - - +
32A LEU* 1.3 60.7 + - - +
34A LEU* 3.6 7.5 + - - +
35A TYR* 3.3 17.2 + - - +
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Residues in contact with LEU 32 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28A ARG 3.4 6.1 + - - +
29A GLU* 3.1 9.9 + - - +
31A LEU* 1.3 74.5 - - - +
33A TYR* 1.3 59.6 + - - +
34A LEU 2.9 2.5 - - - -
35A TYR* 2.5 31.0 + - + -
36A ALA* 2.9 13.1 + - - +
60A GLN* 3.5 40.2 - - + +
61A LYS* 3.5 44.0 - - + +
64A ALA* 3.4 30.7 - - + -
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Residues in contact with TYR 33 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29A GLU 2.9 17.8 + - - +
30A GLN* 3.6 19.3 - - - +
32A LEU* 1.3 77.0 - - - +
34A LEU* 1.3 73.0 + - + +
36A ALA* 4.1 4.4 + - - +
37A ARG* 2.8 53.5 + - - +
64A ALA* 5.7 2.0 - - - -
79A GLU* 2.6 50.3 + - + +
83A VAL* 4.9 7.4 - - + -
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Residues in contact with LEU 34 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19A LEU* 3.5 37.7 - - + -
30A GLN* 3.3 16.6 + - + +
31A LEU 3.9 5.6 - - - +
32A LEU 2.7 4.0 + - - -
33A TYR* 1.3 84.1 - - + +
35A TYR* 1.3 58.6 + - - +
37A ARG* 3.7 0.4 + - - -
38A TYR* 2.8 32.4 + - - +
80A TYR* 3.2 36.1 - - + +
83A VAL* 3.2 37.2 - - + -
84A VAL* 4.5 15.0 - - + -
87A LEU* 5.6 5.8 - - + -
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Residues in contact with TYR 35 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19A LEU* 5.9 0.2 - - - +
31A LEU 3.3 11.8 + - - +
32A LEU* 2.5 26.3 + - + +
34A LEU* 1.3 70.2 - - - +
36A ALA* 1.3 82.5 + - + +
38A TYR* 2.9 10.7 + + - +
39A LYS* 2.7 56.4 + - + +
61A LYS* 3.5 74.0 - - + +
62A TRP 5.1 0.3 + - - -
65A TRP* 3.8 22.4 - - + -
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Residues in contact with ALA 36 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32A LEU 2.9 13.0 + - - +
33A TYR* 4.3 4.5 - - - +
35A TYR* 1.3 79.3 - - - +
37A ARG* 1.3 66.9 + - + +
39A LYS* 2.9 15.4 + - - +
40A GLN 3.0 9.2 + - - -
64A ALA* 3.3 49.1 - - + +
65A TRP* 3.4 10.1 - - - +
68A LEU* 3.4 10.4 - - + +
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Residues in contact with ARG 37 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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33A TYR* 2.8 59.8 + - - +
34A LEU 3.7 2.6 + - - +
35A TYR 3.3 0.2 - - - -
36A ALA* 1.3 79.7 - - + +
38A TYR* 1.3 59.6 + - - +
40A GLN* 2.9 17.0 + - - +
41A VAL* 2.9 19.6 + - - +
68A LEU* 3.5 28.6 - - + +
76A ALA* 3.3 40.0 - - + +
79A GLU* 2.6 50.0 + - - -
80A TYR* 4.2 6.7 - - + +
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Residues in contact with TYR 38 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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12A PHE* 3.3 24.0 - + - -
16A ALA* 5.0 8.3 - - + -
19A LEU* 6.3 0.2 - - + -
34A LEU 2.8 26.4 + - - +
35A TYR* 3.2 11.2 - + - +
37A ARG* 1.3 73.4 - - - +
39A LYS* 1.3 68.0 + - + +
41A VAL* 3.2 10.2 - - - +
42A LYS* 3.0 59.3 + - + +
80A TYR* 3.8 20.6 - + + -
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Residues in contact with LYS 39 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35A TYR* 2.7 49.3 + - + +
36A ALA 3.3 9.0 - - - +
38A TYR* 1.3 88.8 - - + +
40A GLN* 1.3 58.4 + - - +
41A VAL 3.3 0.4 - - - -
42A LYS* 4.5 1.6 - - + +
43A VAL* 2.9 45.2 + - + +
44A GLY 3.1 5.9 + - - -
65A TRP* 3.1 53.7 + - + -
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Residues in contact with GLN 40 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36A ALA 3.0 3.6 + - - -
37A ARG* 2.9 6.6 + - - +
39A LYS* 1.3 77.2 - - - +
41A VAL* 1.3 59.0 + - - +
44A GLY* 3.2 39.5 + - - +
45A ASN* 5.4 1.0 - - - +
65A TRP* 3.7 2.0 - - + +
68A LEU* 2.7 55.4 + - + +
69A GLY 3.9 1.6 + - - -
70A ASP* 4.4 0.7 - - - +
71A SER* 2.4 46.2 + - - +
72A SER 4.1 10.6 - - - +
73A PRO* 4.7 3.1 - - - +
76A ALA* 4.4 4.0 - - + -
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Residues in contact with VAL 41 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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12A PHE* 3.4 31.2 - - + -
37A ARG 2.9 16.1 + - - +
38A TYR 3.2 14.6 - - - +
40A GLN* 1.3 78.4 - - - +
42A LYS* 1.3 71.8 + - + +
43A VAL 5.0 0.2 - - - -
73A PRO* 3.2 34.1 - - + +
76A ALA* 3.1 27.4 - - + -
77A MET* 4.0 16.2 - - + +
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Residues in contact with LYS 42 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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12A PHE* 3.3 28.1 - - - -
13A GLU* 5.2 6.9 + - - -
38A TYR* 3.0 68.5 + - + +
39A LYS* 4.4 2.2 - - + +
41A VAL* 1.3 88.7 - - + +
43A VAL* 1.3 69.4 + - + +
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Residues in contact with VAL 43 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39A LYS* 2.9 41.9 + - + +
40A GLN 4.2 0.4 - - - -
41A VAL 5.0 0.2 - - - -
42A LYS* 1.3 86.2 - - + +
44A GLY* 1.3 59.9 + - - +
45A ASN 4.3 0.5 + - - -
47A ASN* 4.2 20.2 - - - +
65A TRP* 3.8 16.6 - - + -
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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