Contacts of the helix formed by residues 24 - 41 (chain A) in PDB entry 3ECP
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 ASP 24 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22A LEU 3.6 0.2 - - - -
23A GLY* 1.3 81.2 + - - +
25A PRO* 1.3 66.0 - - - +
26A ARG* 2.9 59.5 + - - +
27A ARG* 2.8 59.5 + - + +
28A THR* 3.5 6.6 + - - -
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Residues in contact with PRO 25 (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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24A ASP* 1.3 88.1 - - - +
26A ARG* 1.3 60.2 + - + +
28A THR* 3.3 10.7 + - - +
29A ALA* 2.9 31.6 + - - +
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Residues in contact with ARG 26 (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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24A ASP* 2.9 38.9 + - - +
25A PRO* 1.3 83.1 - - + +
27A ARG* 1.3 57.1 + - + +
29A ALA* 4.1 4.9 - - - +
30A ARG* 3.0 27.8 + - - +
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Residues in contact with ARG 27 (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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22A LEU* 2.9 47.8 + - + -
23A GLY* 3.2 17.6 + - - -
24A ASP* 2.8 34.9 + - + +
26A ARG* 1.3 73.6 - - + +
28A THR* 1.3 56.6 + - - +
30A ARG* 3.3 4.4 + - - -
31A LEU* 2.7 30.3 + - - +
63A PHE* 3.3 12.6 - - + -
66A ASN* 4.4 13.3 - - - +
68A ASN* 3.3 40.8 + - - +
69A VAL* 4.2 19.7 - - + -
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Residues in contact with THR 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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17A PHE 3.3 24.2 - - - +
18A SER* 3.6 24.9 - - - +
20A ALA* 2.8 26.2 + - + +
22A LEU* 4.1 8.6 + - - +
24A ASP 3.5 7.2 + - - -
25A PRO* 3.3 13.0 + - - +
27A ARG* 1.3 76.5 - - - +
29A ALA* 1.3 60.0 + - - +
31A LEU* 3.1 8.5 + - - +
32A VAL* 2.9 33.0 + - + +
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Residues in contact with ALA 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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25A PRO 2.9 17.8 + - - +
26A ARG* 4.1 6.3 - - - +
28A THR* 1.3 74.7 - - - +
30A ARG* 1.3 64.2 + - - +
32A VAL* 3.0 10.9 + - - +
33A ASN* 2.9 33.5 + - - +
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Residues in contact with ARG 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 ARG 3.0 22.2 + - - +
27A ARG* 3.6 5.4 - - - +
28A THR 3.3 0.2 - - - -
29A ALA* 1.3 76.5 - - - +
31A LEU* 1.3 56.2 + - - +
33A ASN* 3.2 25.6 + - - +
34A VAL* 2.9 42.9 + - - +
37A GLN* 5.1 1.8 + - - -
55A ALA 4.5 2.6 + - - -
56A ALA* 4.2 16.8 + - - +
59A GLY* 3.5 38.1 - - - +
60A ALA 4.2 2.0 - - - +
63A PHE* 3.5 28.7 - - + -
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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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17A PHE* 3.4 48.2 - - + +
20A ALA* 3.8 23.8 - - + -
22A LEU* 4.2 8.3 - - + -
27A ARG 2.7 17.8 + - - +
28A THR* 3.2 9.0 - - - +
30A ARG* 1.3 71.1 - - - +
32A VAL* 1.3 55.4 + - - +
34A VAL* 3.3 2.4 + - - +
35A ALA* 2.8 36.4 + - - +
63A PHE* 3.7 26.6 - - + -
74A ILE* 4.3 11.4 - - + -
355A ILE* 3.9 26.7 - - + -
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Residues in contact with VAL 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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10A ALA* 4.8 3.1 - - - +
13A ALA* 3.3 15.1 - - + +
14A LYS* 3.9 37.9 - - + +
17A PHE* 4.1 18.4 - - + -
18A SER* 4.1 17.5 - - - +
28A THR* 2.9 22.5 + - + +
29A ALA* 3.0 11.6 + - - +
31A LEU* 1.3 76.5 - - - +
33A ASN* 1.3 62.8 + - - +
35A ALA* 4.7 0.9 - - - -
36A ALA* 2.9 31.1 + - + +
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Residues in contact with ASN 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 ALA* 2.9 29.3 + - - +
30A ARG* 3.6 31.9 - - - +
32A VAL* 1.3 80.1 - - - +
34A VAL* 1.3 61.1 + - - +
36A ALA* 3.2 7.7 + - - +
37A GLN* 3.0 31.7 + - - +
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Residues in contact with VAL 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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30A ARG* 2.9 38.8 + - + +
31A LEU* 3.7 5.4 - - - +
33A ASN* 1.3 69.5 - - - +
35A ALA* 1.3 67.5 + - - +
37A GLN* 3.2 13.1 - - + +
38A LEU* 3.1 42.5 + - + +
46A ILE* 6.3 1.1 - - + -
60A ALA* 3.7 38.8 - - + +
63A PHE* 4.5 9.2 - - + -
64A ILE* 5.3 3.4 - - + -
352A MET* 5.6 0.9 - - - -
355A ILE* 4.0 19.1 - - + -
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Residues in contact with ALA 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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12A TRP* 3.9 7.3 - - + -
13A ALA* 3.9 8.3 - - + -
17A PHE* 3.6 35.0 - - + -
31A LEU 2.8 20.8 + - - +
32A VAL 3.7 3.8 - - - +
34A VAL* 1.3 73.2 - - - +
36A ALA* 1.3 56.5 + - - +
38A LEU* 3.4 3.3 + - - +
39A ALA* 2.9 32.2 + - - +
355A ILE* 4.1 16.8 - - + +
359A VAL* 4.6 1.4 - - + +
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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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9A ALA* 3.7 11.2 - - + +
10A ALA* 3.9 23.1 - - + -
13A ALA* 3.6 14.1 - - + +
32A VAL* 2.9 19.7 + - + +
33A ASN* 3.4 8.5 - - - +
34A VAL 3.1 0.4 - - - -
35A ALA* 1.3 77.3 - - - +
37A GLN* 1.3 63.5 + - - +
39A ALA* 3.3 1.5 + - - -
40A LYS* 3.0 24.3 + - - +
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Residues in contact with GLN 37 (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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30A ARG* 5.1 1.9 + - - -
33A ASN* 3.0 18.8 + - - +
34A VAL* 3.2 27.6 - - + +
36A ALA* 1.3 75.7 - - - +
38A LEU* 1.3 63.2 + - + +
40A LYS* 3.3 6.2 + - - -
41A TYR* 3.0 31.1 + - + +
46A ILE* 4.0 1.4 + - - +
49A SER* 2.8 41.8 + - - +
50A SER* 3.1 24.9 + - - +
56A ALA* 3.8 25.6 + - - +
60A ALA* 4.4 9.2 - - - +
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Residues in contact with LEU 38 (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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34A VAL* 3.1 35.2 + - + +
35A ALA 3.8 3.6 - - - +
37A GLN* 1.3 76.7 - - + +
39A ALA* 1.3 57.1 - - - +
41A TYR 3.1 4.9 - - - +
42A SER* 3.0 27.9 + - - -
43A GLY 4.6 0.3 + - - -
44A LYS 4.9 6.7 - - - +
46A ILE* 4.2 16.2 - - + +
49A SER* 3.9 21.3 - - - +
352A MET* 3.8 34.8 - - + -
355A ILE* 3.9 25.4 - - + -
356A LEU* 4.3 11.8 - - + +
359A VAL* 4.2 12.8 - - + +
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Residues in contact with ALA 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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9A ALA* 4.3 3.8 - - + -
12A TRP* 3.6 28.3 - - + -
35A ALA 2.9 18.1 + - - +
36A ALA 3.8 3.6 - - - +
38A LEU* 1.3 75.4 - - - +
40A LYS* 1.3 64.1 + - - +
42A SER* 2.6 24.7 + - - -
359A VAL* 4.3 8.2 - - + +
362A ARG* 3.0 29.2 + - - +
450A TRP* 3.5 3.1 - - - -
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Residues in contact with LYS 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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9A ALA* 3.9 15.3 - - + +
36A ALA 3.0 17.2 + - - +
37A GLN* 3.7 7.4 - - - +
39A ALA* 1.3 78.1 - - - +
41A TYR* 1.3 77.6 + - + +
51A GLU* 2.8 29.4 + - - +
362A ARG* 4.9 1.3 - - - +
450A TRP* 3.8 14.5 - - - -
454A GLU* 4.8 6.6 - - - +
461A ASP* 5.9 1.7 + - - -
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Residues in contact with TYR 41 (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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37A GLN* 3.0 28.2 + - + +
38A LEU* 3.1 6.1 - - - +
40A LYS* 1.3 98.6 - - + +
42A SER* 1.3 65.4 + - - +
43A GLY 3.0 0.3 + - - -
44A LYS* 3.0 39.9 + - + +
48A ILE* 4.2 21.3 - - + -
49A SER* 3.6 29.2 - - - -
51A GLU* 2.8 46.7 + - + +
450A TRP* 4.5 1.6 - - - -
454A GLU* 5.8 7.0 - - - -
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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