Contacts of the helix formed by residues 18 - 32 (chain A) in PDB entry 3P1S
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 ARG 18 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13A ALA* 2.8 26.6 + - + +
16A ALA* 3.7 24.7 - - + +
17A GLU* 1.4 70.7 - - - +
19A TYR* 1.3 59.4 + - - +
20A GLU 3.3 2.7 - - - -
21A ASP* 2.9 43.9 + - - +
22A MET 2.9 22.9 + - - -
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Residues in contact with TYR 19 (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 GLU* 4.3 16.9 + - + -
17A GLU* 3.4 50.0 + - + +
18A ARG* 1.3 73.5 - - - +
20A GLU* 1.4 61.5 + - - +
22A MET* 3.4 28.4 - - - +
23A ALA* 2.9 30.5 + - - +
46A VAL* 4.2 11.1 - - + +
47A ALA* 4.0 2.6 - - - +
50A ASN* 3.4 53.0 + - + -
51A VAL* 3.5 12.4 - - + +
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Residues in contact with GLU 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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18A ARG 3.3 0.6 - - - -
19A TYR* 1.4 77.8 - - - +
21A ASP* 1.3 63.6 + - - +
23A ALA* 3.3 3.0 + - - +
24A ALA* 3.0 23.3 + - - +
51A VAL* 3.7 27.0 - - + +
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Residues in contact with ASP 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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13A ALA* 4.1 5.3 - - + +
18A ARG* 2.9 53.9 + - + +
20A GLU* 1.3 75.7 - - - +
22A MET* 1.3 67.3 + - - +
24A ALA* 3.1 7.8 + - - +
25A PHE* 2.8 49.7 + - + -
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Residues in contact with MET 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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10A ALA* 3.4 18.6 - - + +
13A ALA* 3.6 11.4 - - + +
14A GLU* 3.6 31.0 - - + -
18A ARG 2.9 13.7 + - - +
19A TYR* 3.4 31.2 - - - +
21A ASP* 1.3 78.3 - - - +
23A ALA* 1.3 57.1 + - - +
25A PHE* 3.3 5.6 + - - +
26A MET* 2.9 34.2 + - + +
43A LEU* 3.4 50.5 - - + +
46A VAL* 4.1 9.6 - - + -
47A ALA* 3.7 11.0 - - + -
249A FSC 4.9 0.2 - - + -
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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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19A TYR 2.9 17.2 + - - +
20A GLU* 3.7 4.5 - - - +
22A MET* 1.3 75.8 - - - +
24A ALA* 1.3 58.7 + - - +
26A MET* 3.2 2.1 + - - +
27A LYS* 2.8 31.0 + - - +
47A ALA* 3.5 17.3 - - + -
48A TYR* 3.5 37.4 + - + -
51A VAL* 4.2 9.6 - - + -
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Residues in contact with ALA 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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-2A MET* 3.7 27.9 - - + +
20A GLU 3.0 14.6 + - - +
21A ASP* 3.6 9.6 - - - +
23A ALA* 1.3 77.8 - - - +
25A PHE* 1.3 62.2 + - - +
27A LYS* 3.4 9.9 + - - +
28A GLY 3.0 18.0 + - - -
48A TYR* 5.0 0.7 - - - -
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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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-2A MET* 3.6 25.8 - - + -
1A MET* 4.1 8.7 - - + -
6A LEU* 3.5 37.6 - - + +
9A LYS* 3.6 56.8 - - + -
10A ALA* 3.7 5.6 - - + -
13A ALA* 4.3 2.7 - - + -
21A ASP* 2.8 43.6 + - + +
22A MET* 3.7 4.0 - - - +
24A ALA* 1.3 77.1 - - - +
26A MET* 1.4 59.7 + - - +
28A GLY* 3.2 2.9 + - - -
29A ALA* 2.9 26.0 + - - +
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Residues in contact with MET 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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7A ILE* 3.6 33.0 - - + -
10A ALA* 3.5 26.2 - - + -
22A MET* 2.9 22.5 + - + +
23A ALA* 3.9 4.3 - - - +
25A PHE* 1.4 74.8 - - - +
27A LYS* 1.3 66.4 + - - +
29A ALA* 3.1 8.3 + - + +
30A VAL* 2.9 27.4 + - - +
36A LEU* 4.8 6.7 - - + -
40A GLU* 3.4 28.7 - - + +
43A LEU* 3.8 15.5 - - + +
44A LEU* 3.8 37.0 - - + +
47A ALA* 4.8 0.2 - - + -
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Residues in contact with LYS 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 ALA 2.8 15.5 + - - +
24A ALA* 3.6 7.9 - - - +
26A MET* 1.3 71.8 - - - +
28A GLY* 1.3 63.8 + - - +
30A VAL* 3.2 2.8 + - - +
31A GLU* 2.7 63.5 + - - +
44A LEU* 4.5 1.0 - - - +
48A TYR* 3.4 25.8 - - - +
98A THR* 3.6 24.2 - - + -
102A LEU* 4.0 21.3 - - + -
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Residues in contact with GLY 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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-2A MET* 3.7 27.5 - - - +
6A LEU* 3.6 7.4 - - - +
24A ALA 3.0 11.7 + - - -
25A PHE 3.2 4.7 + - - -
27A LYS* 1.3 78.2 - - - +
29A ALA* 1.3 61.2 + - - +
31A GLU* 3.3 19.4 + - - +
32A LYS* 3.3 18.0 + - - +
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Residues in contact with ALA 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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3A ARG* 4.3 14.2 + - + +
6A LEU* 3.7 14.5 - - + +
7A ILE* 3.6 31.4 - - + -
25A PHE 2.9 13.3 + - - +
26A MET* 3.1 15.0 + - + +
28A GLY* 1.3 72.1 - - - +
30A VAL* 1.3 66.6 + - - +
32A LYS* 3.1 23.4 + - - +
33A GLY 4.3 0.5 + - - -
34A GLU 5.0 1.6 - - - +
36A LEU* 4.9 6.8 - - + +
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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 MET* 2.9 17.6 + - + +
27A LYS* 3.6 6.5 - - - +
29A ALA* 1.3 76.4 - - - +
31A GLU* 1.3 59.0 + - - +
32A LYS 3.1 0.2 - - - -
33A GLY* 2.9 22.5 + - - -
34A GLU 4.6 4.2 + - - +
36A LEU* 3.8 35.0 - - + -
44A LEU* 4.1 21.1 - - + -
102A LEU* 3.8 25.8 - - + +
105A SER 4.8 7.1 - - - +
106A HIS 5.3 1.1 - - - +
107A LEU* 3.9 27.5 - - + +
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Residues in contact with GLU 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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-4A GLY 4.3 13.2 + - - +
-2A MET* 5.8 0.7 - - - +
27A LYS* 2.7 58.7 + - - +
28A GLY* 3.7 11.6 - - - +
29A ALA 3.2 0.4 - - - -
30A VAL* 1.3 74.1 - - - +
32A LYS* 1.3 64.3 + - - +
33A GLY* 3.1 2.2 + - - -
102A LEU* 3.9 14.8 - - + +
105A SER 5.8 3.1 - - - +
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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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-2A MET 3.4 7.9 + - - -
-1A GLY* 3.1 27.7 + - - -
1A MET 2.7 29.3 + - - -
2A GLU* 4.9 0.2 - - - +
3A ARG* 3.8 35.4 - - + +
6A LEU* 3.5 17.3 - - - -
28A GLY 3.3 8.6 + - - +
29A ALA* 3.3 16.6 - - - +
30A VAL 3.1 1.0 - - - -
31A GLU* 1.3 77.4 - - - +
33A GLY* 1.4 58.2 + - - +
34A GLU* 3.4 8.9 + - + +
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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