Contacts of the helix formed by residues 22 - 35 (chain S) in PDB entry 3HOU
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 MET 22 (chain S).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1445M ILE* 4.6 6.3 - - + -
1447M GLU* 4.8 17.3 - - + -
1450M LEU* 3.9 16.6 - - + -
13S LEU* 3.6 30.3 - - + -
17S PHE 3.9 11.0 - - - +
18S PHE* 3.5 43.7 - - + -
19S GLY 3.9 11.0 - - - +
20S PRO 3.2 4.3 + - - +
21S ARG* 1.3 73.9 - - - +
23S LYS* 1.3 70.9 + - - +
24S GLN 2.9 0.9 - - - -
25S TYR* 2.6 19.0 + - - +
26S LEU* 3.0 14.8 + - + +
70S PHE* 3.9 24.5 - - + -
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Residues in contact with LYS 23 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1447M GLU* 3.5 39.1 + - + +
20S PRO 5.7 0.7 - - - +
21S ARG* 4.5 12.1 - - - +
22S MET* 1.3 79.6 - - - +
24S GLN* 1.3 63.5 + - - +
26S LEU* 3.3 2.5 + - - +
27S LYS* 3.0 62.5 + - + +
52S ASP 5.3 1.7 + - - -
54S ILE 4.1 8.9 + - - -
55S ASP* 6.0 0.2 - - - +
56S ILE* 4.0 39.5 - - + +
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Residues in contact with GLN 24 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69P ALA 5.4 0.2 + - - -
70P PHE* 6.2 0.4 - - - +
73P SER* 3.4 25.2 + - - +
21S ARG* 3.2 55.0 + - + +
22S MET 2.8 1.8 + - - +
23S LYS* 1.3 81.1 - - - +
25S TYR* 1.3 54.6 + - - +
27S LYS* 3.5 8.1 + - - +
28S THR* 2.6 38.0 + - - +
51S TYR* 4.5 13.5 + - - +
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Residues in contact with TYR 25 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13S LEU* 4.4 12.3 - - + -
17S PHE* 3.4 60.8 - + + -
21S ARG 3.9 10.6 + - - +
22S MET* 2.6 16.5 + - - +
24S GLN* 1.3 74.6 - - - +
26S LEU* 1.3 58.9 + - + +
28S THR* 3.3 15.9 - - + -
29S LYS* 2.9 64.6 + - + +
32S GLU* 5.1 2.2 + - - -
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Residues in contact with LEU 26 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11S ILE* 3.8 28.6 - - + +
13S LEU* 3.9 21.3 - - + -
22S MET* 3.0 16.2 + - + +
23S LYS 3.6 5.4 - - - +
25S TYR* 1.3 74.4 - - + +
27S LYS* 1.3 55.5 + - + +
28S THR 2.7 5.8 + - - -
29S LYS* 2.7 28.5 + - + +
30S LEU* 2.7 13.7 + - - +
56S ILE* 3.1 41.5 - - + -
70S PHE* 3.6 36.6 - - + -
72S VAL* 5.2 9.4 - - + -
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Residues in contact with LYS 27 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21S ARG* 6.2 1.1 - - - +
23S LYS* 3.0 51.6 + - + +
24S GLN* 3.7 3.6 - - - +
26S LEU* 1.3 78.9 - - + +
28S THR* 1.3 58.8 + - - +
30S LEU* 3.5 10.1 - - - +
31S LEU* 3.0 31.3 + - - +
51S TYR* 3.4 49.4 + - + +
52S ASP* 2.9 31.0 + - - +
54S ILE* 3.9 27.1 - - + +
56S ILE* 6.3 0.9 - - + -
72S VAL* 6.1 1.1 - - - -
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Residues in contact with THR 28 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70P PHE* 6.6 0.2 - - + -
24S GLN* 2.6 28.3 + - - +
25S TYR* 3.3 21.9 - - + -
26S LEU 2.7 4.6 + - - -
27S LYS* 1.3 70.8 - - - +
29S LYS* 1.3 69.1 + - - +
31S LEU* 2.9 23.3 + - + +
32S GLU* 2.9 35.2 + - + +
51S TYR* 4.8 3.0 + - - -
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Residues in contact with LYS 29 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11S ILE* 3.7 29.8 - - + -
25S TYR* 2.9 44.6 + - + +
26S LEU* 2.7 14.1 + - + +
28S THR* 1.3 75.3 - - - +
30S LEU* 1.3 67.1 + - - +
32S GLU* 2.9 22.4 + - + +
33S GLU* 2.8 38.5 + - + +
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Residues in contact with LEU 30 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9S LEU* 3.8 25.1 - - + -
11S ILE* 3.6 10.8 - - + +
26S LEU 2.7 14.7 + - - +
27S LYS* 3.5 11.0 - - - +
29S LYS* 1.3 76.3 - - - +
31S LEU* 1.3 54.5 + - + +
33S GLU* 3.0 1.2 + - - +
34S VAL* 2.8 35.3 + - + +
48S VAL* 4.3 5.4 - - + -
54S ILE* 3.7 43.5 - - + -
72S VAL* 3.7 23.8 - - + -
74S TYR* 3.9 35.9 - - + -
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Residues in contact with LEU 31 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66P ARG* 3.8 28.3 - - - +
70P PHE* 4.8 8.1 - - + -
133P THR 5.3 0.9 - - - +
27S LYS 3.0 18.6 - - - +
28S THR* 2.9 14.0 + - + +
30S LEU* 1.3 80.1 - - + +
32S GLU* 1.3 63.7 + - + +
35S GLU* 3.1 38.1 + - + +
48S VAL* 3.4 38.8 - - + -
51S TYR* 3.8 28.0 - - + -
54S ILE* 5.2 1.3 - - + -
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Residues in contact with GLU 32 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25S TYR* 5.1 3.4 + - - -
28S THR* 2.9 29.7 + - + +
29S LYS* 2.9 42.9 + - + +
31S LEU* 1.3 79.6 - - + +
33S GLU* 1.3 63.7 + - + +
35S GLU 4.3 6.4 - - - +
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Residues in contact with GLU 33 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3P VAL* 4.2 27.8 - - - +
9S LEU* 4.2 22.4 - - + +
10S ASN 4.7 2.8 - - - +
11S ILE* 5.0 8.4 - - - +
29S LYS* 2.8 34.8 + - + +
30S LEU 3.9 2.0 - - - +
32S GLU* 1.3 79.6 - - + +
34S VAL* 1.3 63.0 + - - +
37S SER* 4.0 11.4 + - - -
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Residues in contact with VAL 34 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5P THR* 5.1 3.6 - - - +
9S LEU* 3.5 31.0 - - + -
30S LEU* 2.8 15.6 + - + +
33S GLU* 1.3 78.8 - - - +
35S GLU* 1.3 69.2 + - - +
36S GLY 3.0 0.5 + - - -
37S SER* 2.4 30.4 + - - -
45S ILE* 3.2 29.0 - - + +
48S VAL* 4.3 5.6 - - + -
74S TYR* 2.9 50.0 - - + +
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Residues in contact with GLU 35 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66P ARG* 2.6 46.0 + - - -
133P THR 4.5 0.9 - - - +
134P THR* 4.6 0.2 - - - -
135P GLY 4.6 5.2 + - - -
137P ASN* 5.6 3.6 + - - -
138P ASN* 3.2 27.7 + - - +
141P LEU* 4.5 5.0 - - - +
31S LEU* 3.1 27.0 + - - +
32S GLU 4.3 6.6 - - - +
34S VAL* 1.3 75.4 - - - +
36S GLY* 1.3 58.2 + - - +
37S SER 3.6 0.2 + - - -
45S ILE* 3.9 8.5 - - - -
46S LEU 4.0 8.3 - - - +
47S CYS* 3.5 7.6 - - - -
48S VAL* 2.9 35.8 + - + +
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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