Contacts of the helix formed by residues 42 - 57 (chain A) in PDB entry 1GO1
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 ARG 42 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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41A ALA* 1.4 77.5 - - - +
43A PRO* 1.4 72.5 - - + +
44A ASP* 4.0 13.5 - - - +
45A ILE* 3.4 25.5 + - + +
46A LYS* 3.2 22.6 + - - +
81A SER* 4.9 5.1 + - - -
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Residues in contact with PRO 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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41A ALA 3.8 2.7 - - - +
42A ARG* 1.4 88.8 - - + +
44A ASP* 1.4 60.0 + - - +
46A LYS* 3.5 10.6 + - + +
47A GLU* 2.9 35.5 + - - +
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Residues in contact with ASP 44 (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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42A ARG* 4.0 14.4 - - - +
43A PRO* 1.4 80.9 - - - +
45A ILE* 1.4 78.3 + - - +
47A GLU* 4.4 4.2 - - - +
48A ASP* 3.2 31.2 + - - +
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Residues in contact with ILE 45 (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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20A ALA* 3.6 35.7 - - + +
21A ARG 5.7 0.2 - - - +
24A ILE* 4.9 12.8 - - + -
41A ALA* 5.3 2.2 - - + -
42A ARG* 3.4 27.5 + - + +
43A PRO 3.3 0.6 - - - -
44A ASP* 1.4 92.0 - - - +
46A LYS* 1.4 64.2 + - + +
48A ASP* 4.1 2.3 - - - +
49A ILE* 3.2 46.7 + - + +
81A SER* 4.6 11.2 - - - -
82A ALA* 4.8 2.2 - - + -
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Residues in contact with LYS 46 (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 VAL* 4.5 23.7 - - + +
38A ALA 3.5 23.3 - - - +
39A ARG* 3.6 25.1 - - - +
41A ALA* 3.6 19.7 - - + +
42A ARG 3.2 18.9 + - - +
43A PRO* 4.0 7.4 - - + +
45A ILE* 1.4 76.3 - - + +
47A GLU* 1.4 56.8 + - - +
49A ILE* 4.2 1.0 - - - +
50A GLU* 3.0 48.0 + - - +
62A GLU* 4.3 16.7 + - - -
81A SER 5.7 0.2 - - - +
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Residues in contact with GLU 47 (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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43A PRO* 2.9 20.8 + - - +
44A ASP* 4.4 3.4 - - - +
46A LYS* 1.4 73.7 - - - +
48A ASP* 1.4 59.7 + - - +
50A GLU* 4.1 6.8 + - - +
51A TYR* 3.0 34.8 + - + +
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Residues in contact with ASP 48 (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 ILE* 3.2 37.5 - - + +
44A ASP 3.2 21.5 + - - +
45A ILE 4.1 2.5 - - - +
46A LYS 3.4 0.2 - - - -
47A GLU* 1.4 74.7 - - - +
49A ILE* 1.4 59.4 + - - +
51A TYR* 4.7 1.3 - - - -
52A TYR* 3.0 60.3 + - - +
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Residues in contact with ILE 49 (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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20A ALA 3.7 4.3 - - - +
23A SER* 3.7 20.0 - - - +
24A ILE* 3.4 21.5 - - + +
27A ALA* 4.3 3.6 - - + +
35A ILE* 3.5 34.5 - - + -
37A VAL* 4.1 11.4 - - + -
45A ILE* 3.2 34.9 + - + +
46A LYS 4.2 2.0 - - - +
48A ASP* 1.4 74.2 - - - +
50A GLU* 1.4 57.3 + - - +
52A TYR* 4.1 2.8 - - - +
53A ALA* 2.9 34.5 + - + +
60A VAL* 5.2 2.0 - - + -
82A ALA* 3.5 30.5 - - + -
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Residues in contact with GLU 50 (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 VAL* 4.8 8.7 - - + -
46A LYS* 3.0 41.3 + - - +
47A GLU* 4.1 6.7 + - - +
49A ILE* 1.4 72.7 - - - +
51A TYR* 1.4 59.1 + - - +
53A ALA* 3.9 0.5 - - - +
54A ARG* 2.9 37.3 + - - +
60A VAL* 3.9 34.4 - - + +
62A GLU* 4.2 22.4 - - - +
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Residues in contact with TYR 51 (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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47A GLU* 3.0 23.5 + - + +
48A ASP* 4.1 3.1 - - - +
50A GLU* 1.4 78.3 - - - +
52A TYR* 1.4 82.2 + + + +
54A ARG* 3.6 11.4 + - + +
55A LEU* 3.3 40.8 + - + +
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Residues in contact with TYR 52 (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 ILE* 4.7 3.1 - - + +
27A ALA* 3.5 21.7 - - + +
28A LYS* 3.4 47.6 - - + -
48A ASP* 3.0 52.7 + - - +
49A ILE* 4.8 0.7 - - - -
51A TYR* 1.4 96.1 - + - +
53A ALA* 1.4 58.3 - - - +
55A LEU* 3.6 16.1 - - + +
56A SER* 3.0 23.4 + - - -
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Residues in contact with ALA 53 (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 ALA* 3.9 4.4 - - + +
35A ILE* 4.0 21.5 - - + -
49A ILE 2.9 20.4 + - - +
50A GLU 4.0 0.2 - - - +
52A TYR* 1.4 74.4 - - - +
54A ARG* 1.4 63.5 + - - +
56A SER* 3.5 6.3 - - - -
57A GLY 3.1 5.2 + - - -
58A ILE* 2.9 45.9 + - + +
60A VAL* 3.9 15.0 - - + -
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Residues in contact with ARG 54 (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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50A GLU* 2.9 22.1 + - - +
51A TYR* 3.8 9.0 - - + +
52A TYR 3.4 0.4 - - - -
53A ALA* 1.4 76.6 - - - +
55A LEU* 1.4 59.3 + - - +
57A GLY* 3.7 8.0 + - - -
58A ILE 5.0 3.1 + - - -
59A PRO* 6.1 4.4 - - - +
60A VAL* 5.4 7.5 - - - +
99A LYS* 6.3 1.2 - - - +
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Residues in contact with LEU 55 (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 LYS 5.9 2.0 - - - +
51A TYR* 3.3 48.6 + - + +
52A TYR* 3.6 17.7 - - + +
54A ARG* 1.4 76.6 - - - +
56A SER* 1.4 71.8 + - - +
57A GLY* 4.8 0.2 - - - -
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Residues in contact with SER 56 (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 ALA 3.2 23.1 + - - -
28A LYS 4.9 4.7 - - - -
29A MET 5.5 0.4 - - - -
30A GLY* 4.7 8.9 - - - -
52A TYR 3.0 16.2 + - - -
53A ALA* 3.2 10.4 + - - -
55A LEU* 1.4 84.4 - - - +
57A GLY* 1.4 60.1 + - - +
58A ILE* 3.7 13.6 - - - +
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Residues in contact with GLY 57 (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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53A ALA 3.1 5.1 + - - -
54A ARG 3.7 6.2 + - - -
55A LEU 3.5 2.2 - - - -
56A SER* 1.4 78.9 - - - +
58A ILE* 1.4 65.6 + - - +
59A PRO* 4.2 5.1 - - - +
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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