Contacts of the helix formed by residues 34 - 48 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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15C PRO 3.3 13.2 - - - -
16C TYR 3.3 3.1 - - - -
18C MET* 4.3 1.1 - - - -
33C GLU* 1.3 78.7 - - - +
35C TYR* 1.3 67.8 + - - -
36C CYS 3.2 3.1 - - - -
37C LEU* 3.1 2.9 + - - +
38C ASP* 2.9 23.5 + - - -
250C TRP* 3.5 26.3 - - - -
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Residues in contact with TYR 35 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15C PRO 3.0 14.9 + - - +
16C TYR* 4.0 17.9 - + + -
34C GLY* 1.3 71.8 - - - -
36C CYS* 1.3 62.8 + - - +
38C ASP* 3.3 4.1 + - - +
39C LEU* 2.9 30.4 + - + +
105C PHE* 3.5 48.0 + + - -
106C MET* 3.3 24.7 - - + +
243C LEU* 3.9 18.8 + - - +
246C MET* 3.6 39.4 - - + +
247C LYS* 3.6 19.3 - - - -
250C TRP* 3.5 19.5 - - + +
251C TRP* 4.0 12.3 - + + -
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Residues in contact with CYS 36 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16C TYR* 2.8 44.5 + - - +
17C VAL* 3.8 13.2 - - + -
35C TYR* 1.3 79.9 - - - +
37C LEU* 1.3 61.2 + - + +
39C LEU* 4.2 4.0 - - - -
40C LEU* 2.9 30.5 + - - +
86C VAL* 3.5 19.9 - - + +
87C ALA* 3.6 32.1 - - - -
105C PHE* 4.7 7.2 - - - -
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Residues in contact with LEU 37 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10C THR* 5.8 1.8 - - + -
16C TYR 3.9 8.7 - - - +
17C VAL* 4.0 19.1 - - + -
29C ASN* 4.8 4.7 - - + +
32C PHE* 3.7 39.9 - - + +
33C GLU* 3.7 20.2 - - - +
34C GLY 3.1 13.1 + - - +
36C CYS* 1.3 73.7 - - - +
38C ASP* 1.3 64.0 + - - +
40C LEU* 3.7 10.0 - - + +
41C LYS* 2.9 43.2 + - - +
51C TYR* 5.4 4.0 - - + +
53C VAL* 4.1 25.6 - - + -
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Residues in contact with ASP 38 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33C GLU* 6.0 0.2 - - - -
34C GLY 2.9 10.3 + - - +
35C TYR 3.5 8.5 - - - +
37C LEU* 1.3 80.0 - - - +
39C LEU* 1.3 61.3 + - - +
41C LYS* 3.4 15.9 + - - +
42C GLU* 3.0 28.0 + - + +
246C MET* 3.9 19.5 - - + +
249C LYS* 2.8 34.6 + - - +
250C TRP* 2.9 24.9 + - - +
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Residues in contact with LEU 39 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35C TYR* 2.9 20.9 + - + +
36C CYS* 3.6 5.8 - - - +
38C ASP* 1.3 74.8 - - - +
40C LEU* 1.3 59.3 + - - +
42C GLU* 3.2 6.0 + - - +
43C LEU* 2.9 46.2 + - + +
86C VAL* 4.1 13.5 - - + -
105C PHE* 3.8 46.4 - - + -
218C VAL* 4.5 5.8 - - + -
234C ILE* 5.0 5.8 - - + -
237C LEU* 3.8 27.1 - - + -
243C LEU* 4.1 15.5 - - + -
246C MET* 3.5 10.5 - - + +
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Residues in contact with LEU 40 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8C VAL* 3.9 31.2 - - + -
36C CYS 2.9 18.8 + - - +
37C LEU* 3.7 11.2 - - + +
39C LEU* 1.3 74.6 - - - +
41C LYS* 1.3 61.2 + - - +
43C LEU* 3.3 5.3 + - + +
44C SER* 2.9 29.1 + - - -
49C PHE* 4.0 23.3 - - + -
51C TYR* 3.4 36.1 - - + -
53C VAL* 3.7 17.3 - - + -
84C LEU* 4.5 1.1 - - + -
86C VAL* 4.2 21.3 - - + +
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Residues in contact with LYS 41 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20C ARG* 4.5 17.4 - - - +
30C ASP* 5.8 2.9 + - - -
32C PHE 6.0 1.1 - - - -
37C LEU* 2.9 29.3 + - + +
38C ASP* 3.6 15.0 + - - +
40C LEU* 1.3 77.7 - - - +
42C GLU* 1.3 62.0 + - + +
44C SER* 2.7 23.1 + - - -
45C ASN* 3.0 22.9 + - - +
51C TYR* 3.4 19.5 - - - +
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Residues in contact with GLU 42 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38C ASP* 3.0 19.3 + - + +
39C LEU* 3.5 9.0 - - - +
41C LYS* 1.3 76.8 - - + +
43C LEU* 1.3 56.9 + - - +
45C ASN* 3.2 9.5 + - - +
46C ILE* 2.8 45.9 + - - +
237C LEU* 3.8 36.3 - - + +
242C LYS* 4.2 21.1 + - - +
246C MET* 4.6 11.6 - - - +
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Residues in contact with LEU 43 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39C LEU* 2.9 31.9 + - + +
40C LEU* 3.7 8.1 - - - +
42C GLU* 1.3 74.8 - - - +
44C SER* 1.3 58.8 + - - +
46C ILE* 4.6 3.4 - - - +
47C LEU* 2.9 39.4 + - + +
49C PHE* 3.7 13.7 - - + -
84C LEU* 5.0 5.6 - - + -
86C VAL* 4.5 9.6 - - + -
218C VAL* 4.0 29.4 - - + -
230C ILE* 4.3 18.6 - - + +
233C ALA* 3.7 25.8 - - + -
234C ILE* 4.3 11.0 - - + -
237C LEU* 4.5 9.6 - - + -
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Residues in contact with SER 44 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40C LEU 2.9 14.9 + - - -
41C LYS* 2.7 21.1 + - - -
43C LEU* 1.3 75.6 - - - +
45C ASN* 1.3 61.9 + - - +
48C GLY* 2.8 32.9 + - - -
49C PHE* 3.1 31.9 + - - +
51C TYR* 3.4 29.7 - - - -
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Residues in contact with ASN 45 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41C LYS* 3.0 29.2 + - - +
42C GLU* 3.7 10.4 + - - +
44C SER* 1.3 83.2 + - - +
46C ILE* 1.3 66.2 + - + +
47C LEU 3.6 0.3 + - - -
48C GLY* 3.8 5.7 + - - -
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Residues in contact with ILE 46 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42C GLU* 2.8 30.3 + - - +
43C LEU 4.0 2.2 - - - +
45C ASN* 1.3 79.2 - - + +
47C LEU* 1.3 65.0 + - + +
233C ALA* 3.8 28.0 - - + +
236C GLN* 3.7 34.1 - - - +
237C LEU* 3.8 36.1 - - + -
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Residues in contact with LEU 47 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43C LEU* 2.9 20.5 + - + +
46C ILE* 1.3 85.8 - - + +
48C GLY* 1.3 63.9 + - - +
49C PHE* 3.9 18.8 - - + +
226C TYR* 5.0 9.0 - - + +
229C LYS* 3.5 53.4 - - + +
230C ILE* 3.8 29.8 - - + +
232C ILE* 6.0 0.4 - - + -
233C ALA* 4.1 14.4 - - + +
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Residues in contact with GLY 48 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44C SER 2.8 15.0 + - - -
45C ASN* 3.8 5.7 + - - -
46C ILE 3.5 1.2 - - - -
47C LEU* 1.3 81.5 - - - +
49C PHE* 1.3 58.4 + - - +
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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