Contacts of the helix formed by residues 17 - 32 (chain A) in PDB entry 4OUH
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 CYS 17 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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15A ILE* 3.7 2.8 - - - +
16A THR* 1.3 83.1 - - - +
18A ARG* 1.3 65.8 + - - +
19A GLN* 3.4 29.6 - - - +
20A ASP* 3.2 39.8 + - - +
21A ALA 3.4 4.2 + - - -
62A LYS* 3.6 22.7 - - + -
65A TYR* 3.8 0.9 - - - -
117A LEU* 3.5 15.2 - - - +
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Residues in contact with ARG 18 (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 CYS* 1.3 75.3 - - - +
19A GLN* 1.3 69.1 + - - +
21A ALA* 3.1 5.4 + - - +
22A LEU* 3.0 21.7 + - - +
86A GLU 4.9 1.4 + - - -
87A SER* 3.8 23.0 + - - +
108A LEU* 3.7 33.9 - - + +
109A ASP* 2.7 36.4 + - - +
112A ILE* 3.8 41.0 + - + +
114A ALA* 4.0 30.1 - - + +
117A LEU* 3.9 6.4 - - + +
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Residues in contact with GLN 19 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A CYS* 3.2 23.9 - - - +
18A ARG* 1.3 86.1 + - - +
20A ASP* 1.3 56.1 + - - +
22A LEU* 3.2 2.0 + - - +
23A VAL* 2.9 35.0 + - - +
62A LYS* 3.1 24.5 + - - +
63A ASP* 5.3 1.2 + - - -
65A TYR* 3.3 24.2 - - + +
84A THR* 3.4 27.7 + - + +
89A MET* 3.8 18.4 - - - -
108A LEU* 4.0 16.2 - - + +
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Residues in contact with ASP 20 (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 ALA 3.3 6.0 - - - +
15A ILE* 3.8 17.7 - - - -
16A THR* 3.0 20.6 + - - -
17A CYS* 3.2 16.2 + - - +
19A GLN* 1.3 76.6 - - - +
21A ALA* 1.3 57.2 + - - +
24A CYS* 2.9 29.3 + - - +
58A TRP* 3.4 17.3 - - + -
59A ASN* 3.6 5.5 - - - +
62A LYS* 2.8 30.1 + - - -
65A TYR* 2.5 33.1 + - - -
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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
----------------------------------------------------------
8A PHE* 4.5 1.3 - - + -
15A ILE* 4.0 10.3 - - + +
17A CYS 3.4 1.2 + - - -
18A ARG 3.1 9.3 + - - +
20A ASP* 1.3 80.3 - - - +
22A LEU* 1.3 60.9 + - - +
24A CYS* 3.5 3.0 + - - -
25A PHE 3.1 10.2 + - - -
112A ILE* 4.0 6.5 - - + -
117A LEU* 3.9 26.5 - - + -
123A THR* 3.9 13.9 - - + -
124A TYR* 2.7 34.0 + - - +
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Residues in contact with LEU 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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18A ARG 3.0 12.7 + - - +
19A GLN 3.2 7.2 + - - +
21A ALA* 1.3 78.9 - - - +
23A VAL* 1.3 56.4 + - + +
25A PHE* 3.2 6.4 + - + +
26A LEU* 2.9 28.3 + - + +
89A MET* 3.7 26.9 - - + -
91A LEU* 5.3 4.5 - - + -
106A LEU* 4.0 26.0 - - + -
108A LEU* 3.7 26.5 - - + -
111A TYR* 4.7 7.2 - - + -
112A ILE* 4.0 13.6 - - + +
130A LEU* 4.0 37.2 - - + -
134A ILE* 5.4 2.5 - - + -
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Residues in contact with VAL 23 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A GLN 2.9 20.6 + - - +
20A ASP 4.0 2.7 - - - +
22A LEU* 1.3 73.2 - - + +
24A CYS* 1.3 62.0 + - - +
26A LEU* 3.5 12.0 - - + +
27A HIS* 2.8 28.4 + - - +
54A LEU* 5.2 0.7 - - + -
58A TRP* 3.9 20.2 - - + -
65A TYR* 3.6 33.9 - - + -
67A LEU* 3.8 28.5 - - + -
82A ALA* 3.9 17.0 - - + -
89A MET* 4.2 5.8 - - + -
91A LEU* 5.9 0.4 - - + -
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Residues in contact with CYS 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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4A LEU* 4.5 4.0 - - - -
7A LEU* 3.5 33.9 - - - +
8A PHE* 4.2 20.0 - - - -
15A ILE* 4.2 14.1 - - + -
20A ASP 2.9 19.0 + - - +
21A ALA 3.5 6.5 - - - +
23A VAL* 1.3 78.1 - - - +
25A PHE* 1.3 60.6 + - - +
27A HIS* 3.4 5.8 + - - +
28A TRP* 3.3 16.8 + - - +
54A LEU* 4.1 13.7 - - + -
58A TRP* 4.3 5.8 - - + -
124A TYR* 3.9 10.1 - - - +
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Residues in contact with PHE 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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1A MET* 3.6 16.9 - - + +
4A LEU* 3.6 35.9 - - + -
21A ALA 3.1 11.5 + - - +
22A LEU* 3.2 10.7 + - - +
24A CYS* 1.3 77.9 - - - +
26A LEU* 1.3 63.6 + - - +
28A TRP 3.2 1.9 + - - -
29A GLU* 3.1 25.4 + - + +
124A TYR* 3.7 25.6 - + + -
127A SER* 4.0 19.7 - - - -
130A LEU* 3.5 34.5 - - + -
131A ARG* 3.6 32.1 - - + -
134A ILE* 3.9 11.9 - - + -
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Residues in contact with LEU 26 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A LEU* 2.9 15.2 + - + +
23A VAL* 3.5 14.6 - - + +
25A PHE* 1.3 74.7 - - - +
27A HIS* 1.3 65.7 + - - +
29A GLU* 3.2 4.3 + - - +
30A VAL* 3.0 36.1 + - + +
67A LEU* 6.2 1.8 - - + -
69A TYR* 5.9 0.7 - - - +
80A VAL* 3.8 26.5 - - + -
82A ALA* 4.9 6.5 - - + -
91A LEU* 3.9 38.1 - - + -
93A VAL* 6.0 0.2 - - + -
134A ILE* 3.9 35.0 - - + -
138A ILE* 5.0 9.4 - - + -
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Residues in contact with HIS 27 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A LEU* 3.8 18.6 - - + -
23A VAL 2.8 20.3 + - - +
24A CYS 3.5 5.6 - - - +
26A LEU* 1.3 74.6 - - - +
28A TRP* 1.3 57.8 + + - +
30A VAL* 3.3 5.3 + - - +
31A VAL* 2.9 36.3 + - + +
37A GLY* 4.6 4.7 - - - -
52A GLU 2.7 27.8 + - - -
53A LEU 3.6 18.8 + - - -
54A LEU* 3.5 28.9 - - + +
55A PRO* 4.4 7.2 - - + +
67A LEU* 4.9 2.2 - - + +
69A TYR* 2.7 45.8 + + - +
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Residues in contact with TRP 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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1A MET* 3.6 20.4 - - + -
2A ALA 3.0 25.6 + - - -
3A GLY* 3.8 10.8 - - - -
4A LEU* 3.4 23.2 - - + +
7A LEU* 3.8 29.8 - - + -
24A CYS 3.3 3.0 + - - +
25A PHE 3.2 7.9 + - - +
26A LEU 3.2 0.6 - - - -
27A HIS* 1.3 80.2 - + - +
29A GLU* 1.3 55.7 + - - +
31A VAL* 3.7 24.9 - - + -
32A THR* 2.7 64.5 + - + +
52A GLU* 3.7 18.8 - - + -
2B ALA* 4.0 3.4 - - + -
3B GLY* 3.5 39.7 - - - -
6B VAL* 3.8 16.8 - - + -
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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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1A MET* 3.4 22.5 - - + +
25A PHE* 3.1 24.3 + - + +
26A LEU 3.4 9.4 - - - +
28A TRP* 1.3 75.6 - - - +
30A VAL* 1.3 62.4 + - + +
32A THR* 3.1 5.1 + - - -
33A HIS* 2.6 60.1 + - - -
131A ARG* 3.3 38.5 + - - +
134A ILE* 3.9 26.0 - - + -
135A VAL* 3.7 12.1 - - - +
139A ILE* 4.2 2.8 - - + +
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Residues in contact with VAL 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 LEU* 3.0 29.9 + - + +
27A HIS 3.5 7.4 - - - +
28A TRP 3.2 0.2 - - - -
29A GLU* 1.3 75.4 - - - +
31A VAL* 1.3 65.2 + - - +
33A HIS* 3.1 13.5 + - - +
35A TYR* 3.4 40.9 + - + +
69A TYR* 3.6 31.2 - - + +
78A LEU* 4.2 8.5 - - + -
80A VAL* 4.8 11.4 - - + -
138A ILE* 5.4 3.8 - - + -
139A ILE* 4.1 18.4 - - + -
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Residues in contact with VAL 31 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A HIS* 2.9 48.7 + - + +
28A TRP* 3.7 29.4 - - + -
30A VAL* 1.3 75.3 - - - +
32A THR* 1.3 63.3 - - - +
33A HIS 3.1 0.2 - - - -
34A GLY* 3.1 12.1 + - - -
35A TYR 3.3 24.1 + - - +
37A GLY 4.8 2.5 - - - +
52A GLU* 4.0 29.6 - - + +
69A TYR* 4.5 6.7 - - + -
2B ALA* 4.8 7.7 - - + +
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Residues in contact with THR 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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-1A SER* 3.2 22.9 + - - -
0A PRO* 3.6 27.9 + - + +
1A MET* 4.0 2.3 - - - -
2A ALA 4.4 4.7 - - - +
28A TRP* 2.7 59.7 + - + +
29A GLU* 3.1 12.8 + - - -
31A VAL* 1.3 76.1 - - - +
33A HIS* 1.3 62.3 + - - +
34A GLY 3.3 2.4 + - - -
0B PRO* 5.2 6.5 - - + +
2B ALA* 4.7 13.2 - - + -
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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
------------------------------------------------------------
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