Contacts of the helix formed by residues 20 - 36 (chain A) in PDB entry 4PQ6
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 ASP 20 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16A LYS 4.2 0.8 + - - -
17A VAL 3.1 6.1 + - - -
19A ALA* 1.3 82.1 - - + +
21A VAL* 1.3 62.7 + - - +
22A ALA* 3.5 7.3 + - - +
23A GLY* 2.9 27.8 + - - -
24A HIS* 2.8 30.5 + - + +
118A ARG* 4.1 11.5 + - - +
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Residues in contact with VAL 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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17A VAL* 3.7 7.6 - - + +
18A GLU* 3.8 33.6 + - + +
20A ASP* 1.3 72.9 - - - +
22A ALA* 1.3 59.0 + - - +
24A HIS* 3.4 2.0 + - - -
25A GLY* 2.9 26.3 + - - -
66A VAL* 4.0 29.9 - - + +
69A LEU* 3.6 29.7 - - + +
70A THR* 4.7 5.4 - - - +
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Residues in contact with ALA 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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20A ASP* 3.3 5.5 + - - +
21A VAL* 1.3 78.7 - - - +
23A GLY* 1.3 57.3 + - - +
25A GLY* 3.2 2.0 + - - -
26A GLN* 2.9 35.7 + - - +
62A LYS* 3.9 26.1 - - + +
66A VAL* 3.6 23.8 - - + +
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Residues in contact with GLY 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 ASP* 2.9 26.9 + - - -
22A ALA* 1.3 76.0 - - - +
24A HIS* 1.3 62.1 + - - +
26A GLN* 3.4 14.3 + - - +
27A ASP* 3.1 20.4 + - - +
118A ARG* 3.4 21.4 + - - -
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Residues in contact with HIS 24 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A LYS 3.8 6.5 - - - -
17A VAL* 3.5 36.1 + - + -
20A ASP* 2.8 33.8 + - + +
23A GLY* 1.3 75.9 - - - +
25A GLY* 1.3 56.6 + - - +
27A ASP* 3.3 5.5 + - - +
28A ILE* 2.9 38.3 + - + +
69A LEU* 3.8 17.7 - - + -
114A VAL* 4.3 10.5 - - + -
115A LEU* 4.4 4.7 - - + -
118A ARG* 3.5 32.7 + - - -
119A HIS* 2.8 34.9 + + - -
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Residues in contact with GLY 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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21A VAL 2.9 13.6 + - - -
22A ALA 3.2 3.6 + - - -
24A HIS* 1.3 77.4 - - - +
26A GLN* 1.3 61.3 + - - +
28A ILE* 3.3 1.7 + - - +
29A GLU* 3.0 32.1 + - - +
65A GLY* 4.2 11.9 - - - -
69A LEU* 3.5 28.3 - - - +
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Residues in contact with GLN 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 ALA* 2.9 22.6 + - - +
23A GLY* 3.7 13.0 - - - +
25A GLY* 1.3 75.3 - - - +
27A ASP* 1.3 62.1 + - - +
29A GLU* 3.9 4.1 - - - +
30A ILE* 2.9 45.9 + - + +
55A MET 4.8 3.0 + - - +
56A LYS* 3.1 35.6 + - + +
58A SER 4.9 0.8 + - - -
61A LEU* 5.4 5.8 - - + -
62A LYS* 3.8 46.2 - - + +
65A GLY* 5.1 0.2 - - - -
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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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23A GLY 3.1 9.0 + - - +
24A HIS 3.7 4.3 - - - +
26A GLN* 1.3 80.9 - - - +
28A ILE* 1.3 57.9 + - - +
30A ILE* 3.9 5.8 - - - +
31A ARG* 2.9 31.0 + - - +
56A LYS* 4.0 18.7 + - - -
114A VAL* 3.7 21.3 - - + +
118A ARG* 2.8 40.5 + - - +
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Residues in contact with ILE 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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14A TRP* 6.0 2.5 - - + -
17A VAL* 6.0 0.2 - - + -
24A HIS* 2.9 27.1 + - + +
25A GLY* 3.9 4.0 - - - +
27A ASP* 1.3 74.9 - - - +
29A GLU* 1.3 70.3 + - - +
31A ARG* 3.3 3.5 + - - +
32A LEU* 2.9 22.9 + - - +
68A VAL* 6.2 0.7 - - + -
69A LEU* 4.3 21.8 - - + -
107A ILE* 4.1 21.8 - - + -
110A ALA* 3.8 5.6 - - + +
111A ILE* 3.9 39.7 - - + -
114A VAL* 3.7 22.9 - - + -
115A LEU* 4.4 15.7 - - + -
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Residues in contact with GLU 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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25A GLY 3.0 23.7 + - - +
26A GLN 4.0 2.5 - - - +
28A ILE* 1.3 77.6 - - - +
30A ILE* 1.3 62.7 + - - +
32A LEU* 3.2 10.6 + - - +
33A PHE* 3.0 44.4 + - + -
43A PHE* 4.5 8.0 - - - -
61A LEU* 4.0 32.3 - - + +
64A HIS* 3.8 24.4 + - - -
65A GLY* 4.3 12.7 - - - -
68A VAL* 4.3 12.8 - - - +
69A LEU* 5.5 0.9 - - - +
107A ILE* 4.0 21.8 - - - +
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Residues in contact with ILE 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 GLN* 2.9 28.9 + - + +
27A ASP* 4.0 5.8 - - - +
29A GLU* 1.3 77.7 - - - +
31A ARG* 1.3 53.5 + - - +
33A PHE* 3.3 6.4 + - - +
34A LYS* 2.7 65.9 + - + +
52A GLU* 4.0 16.6 - - + +
55A MET* 3.7 33.2 - - + +
56A LYS* 3.5 37.2 - - + +
61A LEU* 4.6 6.7 - - + -
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Residues in contact with ARG 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 2.9 20.1 + - - +
28A ILE 3.7 3.6 - - - +
29A GLU 3.3 0.2 - - - -
30A ILE* 1.3 77.5 - - - +
32A LEU* 1.3 59.1 + - - +
34A LYS* 4.3 7.9 - - - +
35A SER* 2.9 58.8 + - - +
109A GLU 6.1 0.2 - - - -
110A ALA* 3.8 23.9 - - + +
113A HIS* 3.5 52.2 + - + +
114A VAL* 4.4 5.6 - - + -
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Residues in contact with LEU 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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28A ILE 2.9 14.5 + - - +
29A GLU* 3.4 13.0 - - - +
31A ARG* 1.3 77.7 - - - +
33A PHE* 1.3 72.0 + - + +
35A SER* 4.2 2.0 - - - -
36A HIS* 3.0 36.5 + - + +
39A THR* 3.5 25.1 - - + +
43A PHE* 5.1 3.1 - - + -
103A TYR 4.6 1.3 - - - +
106A PHE* 3.7 32.3 - - + +
107A ILE* 3.7 36.6 - - + +
110A ALA* 4.0 8.5 - - + +
201A HEM 4.4 13.9 - - + -
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Residues in contact with PHE 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 GLU* 3.0 44.1 + - + +
30A ILE* 3.9 3.1 - - - +
32A LEU* 1.3 85.0 - - + +
34A LYS* 1.3 63.6 + - - +
36A HIS 4.3 0.2 - - - -
37A PRO* 3.2 27.2 - - - +
39A THR* 3.6 16.8 - - - -
40A LEU* 3.8 37.9 - - + +
43A PHE* 3.6 37.7 - + - -
46A PHE* 4.7 3.8 - + + -
49A LEU* 6.0 0.4 - - + -
55A MET* 3.9 31.0 - - + -
61A LEU* 4.2 19.3 - - + -
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Residues in contact with LYS 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 ILE* 2.7 41.5 + - + +
31A ARG* 3.8 9.0 - - - +
33A PHE* 1.3 79.9 - - - +
35A SER* 1.3 63.6 + - - +
36A HIS 3.6 0.2 + - - -
37A PRO* 3.7 11.5 - - - +
51A THR 5.3 0.2 - - - -
52A GLU* 3.4 51.9 + - - +
55A MET* 4.6 11.0 - - + -
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Residues in contact with SER 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 ARG* 2.9 50.3 + - - -
32A LEU* 5.0 0.2 - - - -
34A LYS* 1.3 78.1 - - - +
36A HIS* 1.3 87.7 + - - +
37A PRO* 3.6 5.1 - - - +
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Residues in contact with HIS 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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32A LEU* 3.0 15.6 + - + +
35A SER* 1.3 99.7 + - - +
37A PRO* 1.3 63.6 - - - +
38A GLU* 3.1 13.1 + - - +
39A THR* 2.8 30.5 + - + -
106A PHE* 3.3 68.3 - + + -
109A GLU* 3.2 23.1 + - + -
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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