Contacts of the helix formed by residues 25 - 38 (chain A) in PDB entry 4GSW
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 SER 25 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23A ASN 3.5 2.5 + - - -
24A ASP* 1.3 77.9 - - - +
26A ILE* 1.3 63.7 + - - +
27A ASP* 3.3 11.2 + - - +
28A ALA* 3.2 24.4 + - - +
29A ILE* 3.5 13.0 + - - +
56A GLY 5.2 0.9 - - - -
57A LYS 3.3 13.2 - - - -
58A THR* 4.0 5.4 - - - +
31B ALA 4.8 0.2 + - - -
34B GLN* 2.9 31.5 + - - -
35B GLU* 2.9 19.0 + - - +
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Residues in contact with ILE 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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25A SER* 1.3 71.6 - - - +
27A ASP* 1.3 62.9 + - - +
29A ILE* 3.0 7.1 + - + +
30A LYS* 3.0 39.1 + - + +
46A LEU* 4.4 7.0 - - + -
53A LEU* 3.7 44.2 - - + +
54A GLU 3.3 34.3 - - - +
55A GLU* 4.3 2.7 - - - +
57A LYS 3.0 18.0 + - - +
58A THR 4.1 10.3 - - - +
59A LEU* 3.9 25.1 - - + -
62A TYR* 4.2 8.1 - - + -
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Residues in contact with ASP 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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25A SER* 3.1 14.7 + - - +
26A ILE* 1.3 76.9 - - - +
28A ALA* 1.3 61.1 + - - +
30A LYS* 3.5 10.1 + - - +
31A ALA* 3.1 22.7 + - - +
41A PRO* 5.7 1.5 - - - +
55A GLU* 3.8 20.1 - - - +
56A GLY* 2.9 29.7 + - - -
31B ALA* 3.7 8.0 - - + +
34B GLN* 3.9 16.7 - - + +
40B PRO* 5.0 1.4 - - - +
41B PRO* 3.3 35.2 - - + +
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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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24A ASP* 4.6 10.3 - - + +
25A SER* 3.2 9.8 + - - +
27A ASP* 1.3 75.8 - - - +
29A ILE* 1.3 67.4 + - + +
31A ALA* 3.4 2.6 + - - +
32A LYS* 3.2 30.7 + - + +
31B ALA* 3.7 15.8 - - + +
35B GLU* 3.5 32.8 - - - +
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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 ILE* 4.5 2.2 - - + -
8A VAL* 4.7 0.2 - - + -
18A LEU* 3.8 18.6 - - + -
20A VAL* 3.4 35.0 - - + -
24A ASP* 4.4 6.5 - - + +
25A SER 3.6 11.2 - - - +
26A ILE* 3.0 11.1 + - + +
28A ALA* 1.3 77.7 - - + +
30A LYS* 1.3 57.8 + - - +
32A LYS* 3.1 7.4 + - + +
33A ILE* 2.9 39.3 + - + +
46A LEU* 4.3 5.8 - - + -
59A LEU* 3.6 32.8 - - + -
70A LEU* 4.1 20.0 - - + -
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Residues in contact with LYS 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 ILE* 3.0 28.1 + - + +
27A ASP* 3.8 7.4 - - - +
29A ILE* 1.3 76.5 - - - +
31A ALA* 1.3 59.3 + - - +
33A ILE* 3.2 1.2 + - - -
34A GLN* 2.8 25.6 + - - +
41A PRO* 3.1 33.1 + - + +
42A ASP* 4.9 0.6 - - - +
44A GLN* 2.8 60.2 + - - +
45A ARG* 5.2 1.3 - - - +
46A LEU* 3.9 15.3 - - + +
52A GLN* 6.0 1.3 - - - +
53A LEU 4.9 5.2 - - - -
55A GLU* 2.8 39.8 + - + +
75A ARG* 4.6 10.1 - - - +
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Residues in contact with ALA 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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27A ASP 3.1 17.9 + - - +
28A ALA 3.7 5.4 - - - +
29A ILE 3.2 0.2 - - - -
30A LYS* 1.3 78.3 - - - +
32A LYS* 1.3 57.7 + - + +
34A GLN* 3.2 9.6 + - - +
35A GLU* 3.0 33.7 + - - +
41A PRO* 4.6 3.8 - - + +
27B ASP* 3.6 36.1 - - + +
28B ALA* 3.9 10.1 - - + +
31B ALA* 4.0 4.0 - - + -
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Residues in contact with LYS 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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18A LEU* 3.8 29.8 - - + -
19A GLU* 2.3 37.1 + - - +
20A VAL* 4.3 11.2 - - + +
24A ASP* 4.9 3.8 + - - -
28A ALA* 3.2 18.8 + - + +
29A ILE* 3.1 9.0 + - + +
31A ALA* 1.3 75.4 - - + +
33A ILE* 1.3 64.3 + - - +
35A GLU* 3.4 18.1 + - - +
36A LYS* 3.3 29.0 + - + +
28B ALA* 6.4 0.9 - - + -
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Residues in contact with ILE 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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8A VAL* 3.8 30.1 - - + -
16A ILE* 4.4 11.2 - - + -
18A LEU* 4.4 4.5 - - + -
29A ILE* 2.9 19.2 + - + +
30A LYS 3.2 1.3 + - - +
32A LYS* 1.3 76.2 - - - +
34A GLN* 1.3 53.3 + - - +
36A LYS 3.2 1.2 + - - -
37A GLU* 2.7 52.3 + - + +
39A ILE* 5.0 1.3 - - + -
44A GLN* 3.5 30.1 - - + +
46A LEU* 3.5 37.9 - - + -
72A LEU* 4.2 14.8 - - + -
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Residues in contact with GLN 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 LYS 2.8 14.2 + - - +
31A ALA* 3.5 8.8 - - - +
32A LYS 3.2 0.2 - - - -
33A ILE* 1.3 77.0 - - - +
35A GLU* 1.3 65.9 + - - +
38A GLY* 2.8 31.4 + - - +
39A ILE 3.3 28.5 - - - +
41A PRO* 4.2 6.1 - - + -
44A GLN* 3.6 1.3 - - - +
25B SER* 2.9 32.5 + - - -
27B ASP* 3.6 12.6 - - - +
55B GLU* 3.7 17.0 - - - +
56B GLY* 3.6 28.3 + - - -
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Residues in contact with GLU 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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31A ALA 3.0 17.6 + - - +
32A LYS* 3.8 22.6 - - - +
33A ILE 3.3 0.4 - - - -
34A GLN* 1.3 81.7 - - - +
36A LYS* 1.3 63.4 + - + +
38A GLY 4.7 0.4 + - - -
23B ASN 5.2 2.5 - - - +
24B ASP* 3.0 22.1 - - - +
25B SER* 2.9 43.2 + - - +
28B ALA* 3.4 10.8 - - - +
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Residues in contact with LYS 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 ILE* 4.2 23.8 - - + +
17A THR 3.9 22.0 + - - +
18A LEU* 4.1 15.9 - - + -
32A LYS* 3.3 15.8 + - - +
33A ILE 3.2 2.5 + - - +
34A GLN 3.1 0.4 - - - -
35A GLU* 1.3 85.4 - - + +
37A GLU* 1.3 67.7 + - - +
38A GLY 3.7 0.4 - - - -
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Residues in contact with GLU 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* 3.7 29.7 + - + +
11A LEU 5.3 0.2 + - - -
12A THR* 5.8 2.8 - - - +
16A ILE* 3.5 33.8 - - + +
33A ILE* 2.7 30.0 + - + +
36A LYS* 1.3 83.1 - - - +
38A GLY* 1.3 60.1 + - - +
39A ILE* 3.4 28.1 + - + +
72A LEU* 4.9 1.1 - - + -
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Residues in contact with GLY 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 GLN* 2.8 24.3 + - - -
35A GLU 4.7 0.2 - - - -
36A LYS 3.7 1.0 - - - -
37A GLU* 1.3 77.4 - - - +
39A ILE* 1.3 61.2 + - - +
40A PRO* 3.6 7.8 - - - +
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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