Contacts of the helix formed by residues 20 - 37 (chain F) in PDB entry 1G3I
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 GLN 20 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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17F ILE* 4.3 2.5 - - + -
18F ILE 4.1 7.4 - - - +
19F GLY* 1.3 76.8 - - - +
21F ALA* 1.3 61.3 + - - +
22F ASP 3.8 0.4 - - - -
23F ALA* 4.1 4.7 - - + +
24F LYS* 3.2 21.1 + - - +
61F VAL* 3.0 29.0 - - - +
66F ILE* 3.9 17.7 - - + -
332F GLU 5.9 0.7 - - - -
333F LEU* 3.1 23.7 - - + +
334F THR* 2.8 59.4 + - - +
336F LEU* 4.5 5.3 - - - +
455F ATP 4.3 2.2 - - - +
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Residues in contact with ALA 21 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10F VAL* 5.6 1.6 - - + +
19F GLY* 4.1 4.0 - - - +
20F GLN* 1.3 71.3 - - - +
22F ASP* 1.3 75.7 + - - +
23F ALA 3.0 1.3 - - - -
24F LYS* 2.8 21.2 + - - +
25F ARG* 2.9 17.1 + - - +
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Residues in contact with ASP 22 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21F ALA* 1.3 79.0 + - - +
23F ALA* 1.3 63.0 + - - +
25F ARG* 3.1 13.8 + - - +
26F ALA* 2.8 22.7 + - - +
331F VAL* 3.5 14.5 - - + +
332F GLU* 4.1 13.9 + - - +
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Residues in contact with ALA 23 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20F GLN* 4.1 9.4 - - - +
21F ALA 3.0 1.0 - - - +
22F ASP* 1.3 79.9 - - - +
24F LYS* 1.3 64.5 + - - +
26F ALA* 2.8 15.0 + - - +
27F VAL* 3.0 17.1 + - - +
55F MET* 4.9 6.7 - - - -
66F ILE* 4.1 12.8 - - + -
331F VAL* 3.2 22.9 - - + +
332F GLU 4.9 1.2 + - - +
333F LEU* 3.8 28.7 - - + -
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Residues in contact with LYS 24 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10F VAL* 4.1 14.8 - - + -
13F LEU* 3.3 43.1 - - + +
14F ASP* 3.0 26.7 + - - +
17F ILE* 2.6 45.9 + - - -
19F GLY* 2.8 25.2 + - - +
20F GLN 3.2 14.3 + - - +
21F ALA* 2.8 13.6 + - - +
23F ALA* 1.3 74.8 - - - +
25F ARG* 1.3 63.8 + - - +
27F VAL* 3.2 7.0 - - - +
28F ALA* 2.9 24.4 + - - +
66F ILE* 4.6 8.9 - - + +
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Residues in contact with ARG 25 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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405E ASP* 4.6 12.3 + - - -
406E LYS* 5.0 9.3 + - - +
409E PHE* 2.8 68.7 - - + +
410E SER* 4.4 7.5 + - - -
10F VAL* 4.3 3.7 - - + +
21F ALA* 2.9 13.5 + - - +
22F ASP* 3.3 15.9 - - - +
24F LYS* 1.3 75.5 - - - +
26F ALA* 1.3 67.8 + - - +
28F ALA* 2.8 16.6 + - - +
29F ILE* 2.8 22.5 + - + +
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Residues in contact with ALA 26 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22F ASP 2.8 11.3 + - - +
23F ALA 2.8 11.0 + - - +
25F ARG* 1.3 79.1 - - - +
27F VAL* 1.3 62.7 + - + +
29F ILE* 3.0 27.3 - - - +
30F ALA* 3.0 9.4 + - - +
53F ILE* 4.0 8.3 - - + +
329F ILE* 4.0 26.0 - - + +
331F VAL* 4.1 17.0 - - + -
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Residues in contact with VAL 27 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13F LEU* 4.1 4.0 - - + -
23F ALA 3.0 10.3 + - - +
24F LYS* 3.2 21.8 - - - +
26F ALA* 1.3 75.0 - - + +
28F ALA* 1.3 57.5 + - - +
30F ALA* 3.5 6.1 - - - +
31F LEU* 2.8 31.2 + - - +
53F ILE* 3.5 19.3 - - + -
55F MET* 4.2 15.5 - - + -
66F ILE* 3.8 17.0 - - + -
67F ALA* 5.6 0.4 - - - -
70F LEU* 3.3 36.5 - - + +
306F ILE* 3.9 12.1 - - + -
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Residues in contact with ALA 28 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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409E PHE* 4.1 2.0 - - + -
6F PRO* 3.4 29.4 - - + +
9F ILE* 3.7 20.6 - - + +
10F VAL* 3.7 10.1 - - + +
24F LYS 2.9 18.2 + - - +
25F ARG* 2.8 6.9 + - - +
27F VAL* 1.3 75.9 - - - +
29F ILE* 1.3 66.1 + - - +
30F ALA 2.9 1.3 + - - -
31F LEU 3.1 1.7 + - - -
32F ARG* 2.8 25.3 + - - +
70F LEU* 4.8 1.1 - - - -
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Residues in contact with ILE 29 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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401E GLU* 4.3 13.0 - - - +
405E ASP* 5.2 12.3 - - - +
408E SER* 4.2 17.7 - - - +
409E PHE* 3.4 46.2 - - + +
6F PRO* 4.8 3.6 - - - -
25F ARG* 2.8 17.2 + - + +
26F ALA* 3.0 22.7 - - - +
28F ALA* 1.3 71.1 - - - +
30F ALA* 1.3 62.6 + - - +
32F ARG* 3.2 7.8 + - - +
33F ASN* 2.8 35.8 + - - +
36F ARG* 5.0 0.9 + - - -
329F ILE* 4.0 21.5 - - + -
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Residues in contact with ALA 30 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26F ALA 3.1 16.2 - - - +
27F VAL* 3.5 9.6 - - - +
29F ILE* 1.3 80.9 - - + +
31F LEU* 1.3 64.3 + - - +
32F ARG 3.0 1.5 + - - -
33F ASN* 3.5 16.1 + - - +
34F ARG* 3.7 10.4 + - - +
51F LYS* 5.3 6.1 - - + +
53F ILE* 3.9 16.8 - - + -
304F LEU* 4.3 20.2 - - + +
329F ILE* 5.0 5.2 - - + -
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Residues in contact with LEU 31 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3F GLU* 5.4 16.8 - - + +
4F MET* 6.1 0.7 - - + -
9F ILE* 3.9 13.2 - - + -
27F VAL 2.8 21.8 + - - +
28F ALA 3.9 2.5 - - - +
30F ALA* 1.3 73.4 - - - +
32F ARG* 1.3 63.3 + - - +
34F ARG* 3.1 34.4 - - + +
35F TRP* 4.0 3.1 + - - +
70F LEU* 3.9 18.6 - - + -
73F LEU* 3.9 20.0 - - + -
74F ALA* 3.3 35.7 - - + -
251F ASN* 5.9 2.5 - - + -
253F ILE* 5.6 5.2 - - + -
304F LEU* 4.9 5.1 - - + +
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Residues in contact with ARG 32 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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363E GLU* 2.7 43.1 + - - +
412E SER* 3.8 6.9 + - - -
3F GLU* 3.7 10.5 + - - -
4F MET 2.8 31.0 + - - -
5F THR* 3.9 6.0 - - - +
6F PRO* 3.4 34.0 - - + +
9F ILE* 4.5 3.7 - - + +
28F ALA 2.8 16.7 + - - +
29F ILE* 3.4 5.2 - - - +
30F ALA 3.0 0.2 - - - -
31F LEU* 1.3 74.8 - - - +
33F ASN* 1.3 56.1 + - - +
34F ARG 2.7 15.1 + - - -
35F TRP* 2.8 65.8 + - - +
36F ARG* 3.1 14.9 + - - +
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Residues in contact with ASN 33 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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356E TYR* 5.7 4.8 - - - -
359E LEU* 4.2 16.6 - - + +
360E MET* 4.8 0.3 - - - +
401E GLU* 4.8 6.5 + - - -
408E SER* 4.1 11.2 + - - -
29F ILE* 2.8 23.6 + - - +
30F ALA* 4.0 8.7 - - - +
31F LEU 3.5 0.4 - - - -
32F ARG* 1.3 74.7 - - - +
34F ARG* 1.3 61.6 + - - +
36F ARG* 3.1 32.6 + - - +
37F ARG* 3.0 25.5 + - - +
50F PRO* 6.4 1.6 - - + -
51F LYS* 4.2 24.8 - - + +
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Residues in contact with ARG 34 (chain F).
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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30F ALA 3.7 7.2 + - - +
31F LEU* 3.1 30.6 + - + +
32F ARG 2.7 1.6 + - - -
33F ASN* 1.3 80.6 - - - +
35F TRP* 1.3 52.9 + - - +
37F ARG* 2.6 32.5 + - - +
38F MET* 3.5 31.8 - - + +
50F PRO* 4.9 5.5 - - - +
250F GLN 3.2 14.0 + - - +
251F ASN* 2.8 44.4 - - + +
252F GLY 3.1 3.8 + - - +
253F ILE* 2.8 29.0 - - - +
302F HIS* 3.1 26.8 + - - -
304F LEU* 3.7 20.0 - - - +
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Residues in contact with TRP 35 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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362E THR* 3.7 29.4 - - + -
363E GLU* 3.5 14.8 - - - -
2F SER* 3.6 24.7 - - - -
3F GLU* 3.9 29.8 - - + -
31F LEU 4.0 0.6 + - - +
32F ARG* 2.8 63.1 + - - +
34F ARG* 1.3 73.4 - - - +
36F ARG* 1.3 86.0 + - + +
37F ARG 2.8 10.3 - - - +
38F MET* 4.2 1.9 - - - -
39F GLN* 3.0 57.3 + - - +
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Residues in contact with ARG 36 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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359E LEU* 3.4 18.6 - - + +
360E MET* 3.0 28.8 - - - +
362E THR* 3.9 14.1 - - - +
363E GLU* 2.7 41.1 + - + +
408E SER* 2.4 43.8 + - - -
409E PHE 4.3 0.8 + - - -
411E ALA* 4.0 4.9 - - - +
6F PRO* 3.9 7.1 - - - +
29F ILE 5.0 1.5 + - - -
32F ARG* 3.1 22.8 + - - +
33F ASN* 3.1 26.3 + - - +
35F TRP* 1.3 90.8 - - + +
37F ARG* 1.3 60.1 + - - +
39F GLN* 2.6 30.7 + - - +
40F LEU* 3.8 3.8 + - - +
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Residues in contact with ARG 37 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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359E LEU* 3.4 6.0 - - + +
33F ASN 3.0 14.9 + - - +
34F ARG* 2.6 27.2 + - - +
35F TRP 2.8 5.2 - - - +
36F ARG* 1.3 81.6 - - - +
38F MET* 1.3 96.0 + - - +
40F LEU* 3.3 15.3 - - + -
45F ARG* 2.8 29.0 + - - +
46F HIS* 4.7 4.9 + - - -
48F VAL* 3.2 44.2 - - + -
49F THR* 5.6 0.9 - - - +
50F PRO* 6.1 0.9 - - - -
250F GLN* 3.2 30.1 + - - +
302F HIS* 3.4 36.8 + - - +
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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