Contacts of the helix formed by residues 34 - 48 (chain A) in PDB entry 3GBA
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 GLY 34 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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15A PRO 3.3 13.9 - - - -
16A TYR 3.3 3.8 - - - -
18A MET* 4.4 0.7 - - - -
33A GLU* 1.3 78.3 - - - +
35A TYR* 1.3 67.1 + - - -
36A CYS 3.2 2.7 - - - -
37A LEU* 3.1 2.8 + - - +
38A ASP* 3.0 25.2 + - - -
250A TRP* 3.4 24.5 - - - -
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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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15A PRO 3.0 15.2 + - - +
16A TYR* 3.2 21.5 + + + -
34A GLY* 1.3 71.8 - - - -
36A CYS* 1.3 63.4 + - - +
38A ASP* 3.2 3.9 + - - +
39A LEU* 2.9 29.6 + - + +
105A PHE* 3.7 39.8 + + - -
106A MET* 3.3 24.3 - - + +
243A LEU* 4.0 19.4 + - - +
246A MET* 3.6 49.5 - - + +
247A LYS* 3.9 9.0 - - + -
250A TRP* 3.5 19.0 - - + +
251A TRP* 3.8 17.7 - + + -
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Residues in contact with CYS 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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16A TYR* 2.9 41.2 + - - +
17A VAL* 3.8 13.0 - - + -
35A TYR* 1.3 81.4 - - - +
37A LEU* 1.3 62.6 + - + +
39A LEU* 3.7 4.7 - - - +
40A LEU* 2.9 30.4 + - - +
86A VAL* 3.7 19.5 - - + +
87A ALA* 3.6 32.5 - - - -
105A PHE* 4.9 6.1 - - - -
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Residues in contact with LEU 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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10A THR* 5.9 0.2 - - + -
16A TYR 3.9 8.5 - - - +
17A VAL* 3.9 18.4 - - + -
29A ASN* 4.7 5.2 - - + +
32A PHE* 3.8 38.4 - - + +
33A GLU* 3.8 20.6 - - - +
34A GLY 3.1 11.8 + - - +
36A CYS* 1.3 74.8 - - + +
38A ASP* 1.3 63.5 + - - +
40A LEU* 3.7 8.6 - - + +
41A LYS* 2.9 29.1 + - - +
51A TYR* 4.7 6.7 + - + +
53A VAL* 3.9 28.3 - - + -
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Residues in contact with ASP 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 GLY 3.0 16.3 + - - +
35A TYR 3.6 7.9 - - - +
37A LEU* 1.3 76.5 - - - +
39A LEU* 1.3 65.6 + - - +
41A LYS* 3.3 9.2 + - - +
42A GLU* 3.1 29.3 + - + +
245A MET* 5.6 2.3 - - + +
246A MET* 4.1 19.4 - - + +
249A LYS* 2.8 35.0 + - - +
250A TRP* 2.9 17.5 + - - +
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Residues in contact with LEU 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* 2.9 16.7 + - + +
36A CYS* 3.7 7.0 - - - +
38A ASP* 1.3 75.9 - - - +
40A LEU* 1.3 55.4 + - - +
42A GLU* 3.2 4.0 + - - +
43A LEU* 2.9 46.6 + - + +
86A VAL* 4.2 14.4 - - + -
105A PHE* 3.9 44.6 - - + -
218A VAL* 4.4 7.4 - - + -
234A ILE* 5.0 6.7 - - + -
237A LEU* 3.9 24.5 - - + -
243A LEU* 4.4 9.6 - - + -
246A MET* 3.5 23.6 - - + +
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Residues in contact with LEU 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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8A VAL* 4.1 27.8 - - + -
36A CYS 2.9 17.7 + - - +
37A LEU* 3.7 9.6 - - + +
39A LEU* 1.3 77.7 - - - +
41A LYS* 1.3 57.3 + - - +
43A LEU* 3.3 7.6 + - + +
44A SER* 2.9 31.7 + - - -
49A PHE* 3.9 27.4 - - + -
51A TYR* 3.4 35.7 - - + -
53A VAL* 3.7 18.2 - - + -
84A LEU* 4.9 1.1 - - + -
86A VAL* 4.3 18.4 - - + -
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Residues in contact with LYS 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 LEU 2.9 17.5 + - - +
38A ASP* 3.6 9.2 - - - +
39A LEU 3.3 0.2 - - - -
40A LEU* 1.3 75.6 - - - +
42A GLU* 1.3 64.4 + - + +
44A SER* 2.7 24.3 + - - +
45A ASN* 3.0 27.1 + - - +
51A TYR* 3.9 15.7 + - - +
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Residues in contact with GLU 42 (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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38A ASP* 3.1 19.0 + - + +
39A LEU 3.6 6.1 - - - +
41A LYS* 1.3 78.9 - - + +
43A LEU* 1.3 62.0 + - - +
45A ASN* 3.3 12.3 + - - +
46A ILE* 3.0 31.2 + - - +
237A LEU* 3.8 25.8 - - + +
242A LYS* 3.2 40.0 + - - +
245A MET* 4.6 11.4 - - - +
246A MET* 4.6 11.4 - - - +
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Residues in contact with LEU 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 LEU* 2.9 39.3 + - + +
40A LEU* 3.8 9.2 - - + +
42A GLU* 1.3 75.0 - - - +
44A SER* 1.3 58.6 + - - +
46A ILE* 3.4 3.9 + - - -
47A LEU* 2.8 37.6 + - + +
49A PHE* 3.8 13.7 - - + -
84A LEU* 5.8 0.4 - - + -
86A VAL* 4.9 8.3 - - + -
218A VAL* 4.2 11.7 - - + -
230A ILE* 4.1 36.8 - - + +
233A ALA* 3.7 27.1 - - + -
234A ILE* 4.5 3.6 - - + -
237A LEU* 4.2 14.1 - - + -
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Residues in contact with SER 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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40A LEU 2.9 14.9 + - - -
41A LYS* 2.7 21.8 + - - +
43A LEU* 1.3 76.9 - - - +
45A ASN* 1.3 62.2 + - - +
48A GLY* 2.8 24.1 + - - -
49A PHE* 3.2 42.0 + - - +
51A TYR* 3.5 26.0 - - - -
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Residues in contact with ASN 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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41A LYS* 3.0 37.0 + - - +
42A GLU* 3.7 13.8 + - - +
43A LEU 3.2 0.2 - - - -
44A SER* 1.3 88.1 + - - +
46A ILE* 1.3 65.6 + - + +
48A GLY* 3.5 6.8 + - - -
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Residues in contact with ILE 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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42A GLU* 3.0 23.3 + - - +
43A LEU 3.9 2.2 - - - +
45A ASN* 1.3 79.1 - - + +
47A LEU* 1.3 68.8 + - + +
233A ALA* 4.0 25.8 - - + +
236A GLN* 3.7 38.1 - - - +
237A LEU* 3.9 32.3 - - + -
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Residues in contact with LEU 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 LEU* 2.8 25.8 + - + +
46A ILE* 1.3 91.8 - - + +
48A GLY* 1.3 62.9 + - - +
49A PHE* 3.5 21.7 - - + +
226A TYR* 5.2 9.1 - - + -
229A LYS* 3.8 43.1 - - + +
230A ILE* 3.7 31.2 - - + -
232A ILE* 6.5 0.2 - - + -
233A ALA* 4.3 6.5 - - + -
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Residues in contact with GLY 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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3A ASN* 5.0 8.0 - - - +
44A SER 2.8 14.7 + - - -
45A ASN 3.5 5.4 + - - -
46A ILE 3.5 3.0 + - - -
47A LEU* 1.3 80.2 - - - +
49A PHE* 1.3 56.9 + - - +
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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