Contacts of the helix formed by residues 20 - 37 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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17A ILE* 4.3 3.6 - - + -
18A ILE 4.0 7.0 - - - +
19A GLY* 1.3 78.1 - - - +
21A ALA* 1.3 63.0 + - - +
22A ASP 3.8 0.4 - - - -
23A ALA* 4.0 5.1 - - + +
24A LYS* 3.3 21.3 + - - +
61A VAL* 3.0 26.8 - - - +
66A ILE* 3.9 17.7 - - + -
332A GLU 5.8 1.1 - - - -
333A LEU* 2.9 24.2 - - + +
334A THR* 2.5 62.3 + - - +
336A LEU* 4.6 6.1 - - + +
450A ATP 4.6 0.4 - - - +
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Residues in contact with ALA 21 (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 VAL* 5.8 1.7 - - + +
19A GLY* 4.3 4.0 - - - -
20A GLN* 1.3 72.4 - - - +
22A ASP* 1.3 75.1 + - - +
23A ALA 2.9 1.6 - - - -
24A LYS* 2.6 23.6 + - - +
25A ARG* 2.8 15.6 + - - +
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Residues in contact with ASP 22 (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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21A ALA* 1.3 78.7 + - - +
23A ALA* 1.3 63.6 + - - +
25A ARG* 3.2 12.2 + - - +
26A ALA* 2.9 24.3 + - - +
331A VAL* 3.5 15.8 - - + +
332A GLU* 4.1 15.5 + - - +
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Residues in contact with ALA 23 (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 GLN 4.0 6.0 - - - +
21A ALA 2.8 1.4 + - - +
22A ASP* 1.3 82.5 - - - +
24A LYS* 1.3 62.8 + - - +
26A ALA* 3.2 3.3 + - - +
27A VAL* 3.0 26.5 + - - +
55A MET* 5.0 4.7 - - - +
66A ILE* 3.8 25.1 - - + -
331A VAL* 3.4 15.3 - - + +
332A GLU 4.8 1.2 + - - +
333A LEU* 3.8 29.6 - - + -
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Residues in contact with LYS 24 (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 VAL* 4.3 13.9 - - + -
13A LEU* 3.4 41.4 - - + +
14A ASP* 3.1 27.5 + - - +
17A ILE* 2.7 50.1 + - - -
19A GLY* 2.8 24.3 + - - +
20A GLN 3.3 12.8 + - - +
21A ALA* 2.6 15.0 + - - +
23A ALA* 1.3 74.0 - - - +
25A ARG* 1.3 64.8 + - - +
27A VAL* 2.9 9.6 - - - +
28A ALA* 2.9 22.5 + - - +
66A ILE* 4.5 8.5 - - + -
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Residues in contact with ARG 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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10A VAL* 4.2 6.3 - - + +
21A ALA* 2.8 11.7 + - - +
22A ASP* 3.3 15.0 - - - +
24A LYS* 1.3 75.1 - - - +
26A ALA* 1.3 56.0 + - - +
28A ALA* 2.4 37.4 + - - +
29A ILE* 2.8 14.1 + - + +
405F ASP* 4.2 16.8 + - - -
406F LYS* 5.4 7.9 + - - +
409F PHE* 2.9 64.9 - - + +
410F SER* 5.0 3.0 + - - -
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Residues in contact with ALA 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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22A ASP 2.9 16.2 + - - +
23A ALA 3.3 10.3 - - - +
25A ARG* 1.3 73.2 - - - +
27A VAL* 1.3 62.6 + - + +
29A ILE* 3.2 16.9 - - - +
30A ALA* 3.1 21.7 + - - +
53A ILE* 3.9 8.9 - - + +
329A ILE* 4.2 17.2 - - + +
331A VAL* 4.1 23.1 - - + -
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Residues in contact with VAL 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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13A LEU* 3.9 10.1 - - + -
23A ALA 3.3 9.9 - - - +
24A LYS* 2.9 24.5 - - - +
26A ALA* 1.3 75.7 - - + +
28A ALA* 1.3 57.6 + - - +
30A ALA* 3.5 7.5 - - - +
31A LEU* 2.8 28.1 + - - +
53A ILE* 3.6 19.1 - - + -
55A MET* 3.9 24.7 - - + -
66A ILE* 3.7 17.5 - - + +
70A LEU* 3.5 22.7 - - + +
306A ILE* 3.9 12.6 - - + -
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Residues in contact with ALA 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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6A PRO* 3.6 28.3 - - + +
9A ILE* 4.0 20.1 - - + +
10A VAL* 3.8 10.1 - - + +
24A LYS 2.9 13.0 + - - +
25A ARG* 2.4 30.5 + - - +
27A VAL* 1.3 65.3 - - - +
29A ILE* 1.3 57.5 + - - +
30A ALA 2.8 0.7 - - - -
31A LEU* 2.6 25.1 + - - +
32A ARG* 2.7 14.1 + - - +
409F PHE* 4.6 1.6 - - + -
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Residues in contact with ILE 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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6A PRO* 4.8 4.9 - - - +
25A ARG* 2.8 16.8 + - + +
26A ALA* 3.2 20.9 - - - +
28A ALA* 1.3 71.5 - - - +
30A ALA* 1.3 63.6 + - + +
32A ARG* 3.1 8.9 + - - +
33A ASN* 2.9 37.4 + - - +
36A ARG* 5.1 0.7 + - - -
329A ILE* 4.1 20.6 - - + -
401F GLU* 4.5 12.1 - - + +
405F ASP* 5.1 13.7 - - - +
408F SER* 4.6 17.5 - - - +
409F PHE* 3.7 38.6 - - + +
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Residues in contact with ALA 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 ALA 3.1 16.6 + - - +
27A VAL* 3.5 9.4 - - - +
28A ALA 2.8 0.8 + - - -
29A ILE* 1.3 85.6 - - + +
31A LEU* 1.3 62.8 + - - +
32A ARG 3.2 0.7 + - - -
33A ASN* 3.3 16.7 + - - +
34A ARG* 3.6 8.1 + - - +
51A LYS* 5.8 5.2 - - + +
53A ILE* 4.0 16.2 - - + -
304A LEU* 4.3 19.5 - - + +
329A ILE* 5.0 5.4 - - + -
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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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3A GLU* 5.6 15.5 - - + +
4A MET* 6.2 0.2 - - + -
9A ILE* 3.7 23.3 - - + -
27A VAL 2.8 17.5 + - - +
28A ALA 2.6 10.2 + - - +
30A ALA* 1.3 72.7 - - - +
32A ARG* 1.3 61.2 + - - +
34A ARG* 3.1 36.3 - - + +
35A TRP* 3.9 2.3 + - - +
70A LEU* 3.7 23.8 - - + -
73A LEU* 4.0 9.2 - - + -
74A ALA* 3.5 33.4 - - + -
251A ASN* 6.1 1.6 - - + -
253A ILE* 5.5 4.0 - - + -
304A LEU* 5.1 3.8 - - + +
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Residues in contact with ARG 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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3A GLU* 3.9 9.6 + - - -
4A MET 2.9 28.3 + - - -
5A THR* 4.1 7.7 - - - +
6A PRO* 3.5 32.4 - - + +
9A ILE* 4.5 3.1 - - + +
28A ALA 2.7 11.2 + - - +
29A ILE* 3.4 9.0 - - - +
30A ALA 3.0 0.2 - - - -
31A LEU* 1.3 74.1 - - - +
33A ASN* 1.3 53.2 + - - +
34A ARG 2.6 15.9 + - - -
35A TRP* 2.6 67.7 + - - +
36A ARG* 3.2 16.2 + - - +
363F GLU* 2.6 41.8 + - - +
412F SER* 3.5 9.8 + - - -
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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 ILE* 2.9 26.6 + - - +
30A ALA* 3.3 11.3 + - - +
32A ARG* 1.3 71.4 - - - +
34A ARG* 1.3 62.5 + - - +
36A ARG* 3.0 35.4 + - - +
37A ARG* 3.0 25.8 + - - +
51A LYS* 4.5 20.9 - - + +
356F TYR* 5.9 5.2 - - - -
359F LEU* 4.3 12.6 - - + +
360F MET* 4.9 0.7 - - - +
401F GLU* 4.6 8.7 + - - -
408F SER* 3.8 9.7 + - - -
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Residues in contact with ARG 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 ALA 3.6 5.0 + - - +
31A LEU* 3.1 29.7 + - + +
32A ARG 2.6 5.5 + - - -
33A ASN* 1.3 77.2 - - - +
35A TRP* 1.3 56.0 + - - +
37A ARG* 2.8 29.6 - - - +
38A MET* 3.6 30.1 - - + +
50A PRO* 5.0 4.2 - - - +
250A GLN 3.3 15.4 + - - +
251A ASN* 2.8 44.3 + - + +
252A GLY 3.3 3.0 + - - +
253A ILE* 2.9 29.3 - - - +
302A HIS* 3.2 25.9 + - - -
304A LEU* 3.5 21.9 - - - +
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Residues in contact with TRP 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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2A SER* 3.5 25.7 - - - -
3A GLU* 3.9 29.8 - - + -
31A LEU 3.9 0.9 + - - +
32A ARG* 2.6 63.4 + - - +
34A ARG* 1.3 76.0 - - - +
36A ARG* 1.3 75.0 + - + +
37A ARG 2.7 13.7 - - - +
38A MET* 4.1 3.2 - - - -
39A GLN* 3.2 45.6 + - - +
362F THR* 4.0 24.2 - - + -
363F GLU* 3.2 22.2 - - + -
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Residues in contact with ARG 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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6A PRO* 4.2 4.9 - - - +
29A ILE 5.1 0.6 + - - -
32A ARG* 3.2 19.9 + - - +
33A ASN* 3.0 26.9 + - - +
35A TRP* 1.3 92.0 - - + +
37A ARG* 1.3 62.9 + - - +
39A GLN* 2.8 22.7 + - - +
40A LEU* 3.5 8.8 - - - +
359F LEU* 3.3 20.4 - - + +
360F MET* 3.1 27.1 - - - +
362F THR* 3.6 13.0 + - - +
363F GLU* 2.8 35.1 + - + +
408F SER* 2.5 51.1 + - - -
411F ALA* 3.9 6.5 - - - +
412F SER 4.3 2.0 - - - +
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Residues in contact with ARG 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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33A ASN 3.0 14.3 + - - +
34A ARG* 2.8 12.4 + - - +
35A TRP 2.7 13.7 - - - +
36A ARG* 1.3 77.5 - - - +
38A MET* 1.3 111.5 + - - +
39A GLN 2.8 6.1 - - - -
40A LEU* 3.2 14.8 - - + -
45A ARG* 3.0 23.6 + - - +
46A HIS* 4.6 4.0 + - - -
48A VAL* 3.4 42.2 - - + -
49A THR* 5.6 1.8 - - - +
50A PRO* 6.0 0.9 - - - -
250A GLN* 3.1 30.1 + - - +
302A HIS* 3.2 41.3 + - - +
359F LEU* 3.5 5.3 - - + +
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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