Contacts of the helix formed by residues 4 - 25 (chain A) in PDB entry 3P9K
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 THR 4 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5A ALA* 1.3 59.7 + - - +
6A ALA 3.1 3.7 - - - +
7A ASP* 2.5 32.2 + - + +
8A MET* 2.4 64.6 + - + +
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Residues in contact with ALA 5 (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 THR* 1.3 83.0 + - - +
6A ALA* 1.3 59.2 + - - +
8A MET* 4.0 10.3 - - - +
9A ALA* 3.3 24.8 + - - +
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Residues in contact with ALA 6 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A THR 2.9 1.0 + - - +
5A ALA* 1.3 76.8 - - - +
7A ASP* 1.3 64.4 + - - +
8A MET 3.2 0.7 - - - -
9A ALA* 4.3 3.1 - - - +
10A ALA* 3.0 32.9 + - - +
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Residues in contact with ASP 7 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A THR* 2.5 33.1 + - + +
6A ALA* 1.3 77.1 - - - +
8A MET* 1.3 58.5 - - + +
10A ALA* 4.2 5.2 - - - +
11A SER* 3.7 17.7 + - - -
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Residues in contact with MET 8 (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 THR* 2.4 63.2 + - + +
5A ALA* 4.0 8.1 - - - +
7A ASP* 1.3 70.2 - - + +
9A ALA* 1.3 60.8 + - - +
10A ALA 3.2 1.8 - - - -
11A SER* 3.5 4.5 + - - -
12A ALA* 2.9 30.0 + - - +
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Residues in contact with ALA 9 (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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5A ALA 3.3 18.1 + - - +
6A ALA* 4.3 3.6 - - - +
8A MET* 1.3 77.9 - - - +
10A ALA* 1.3 60.1 + - - +
12A ALA* 3.9 5.6 - - - -
13A ASP* 2.7 37.7 + - - +
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Residues in contact with ALA 10 (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 ALA 3.0 20.3 + - - +
7A ASP* 4.6 5.4 - - - +
9A ALA* 1.3 77.1 - - - +
11A SER* 1.3 64.1 + - - +
13A ASP* 3.4 5.8 + - - +
14A GLU* 3.1 22.7 + - - +
350B TYR* 4.2 5.2 + - - -
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Residues in contact with SER 11 (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 ASP 3.7 16.5 + - - -
8A MET* 3.5 6.2 + - - -
10A ALA* 1.3 76.6 - - - +
12A ALA* 1.3 63.9 + - - +
14A GLU* 3.2 9.2 + - - +
15A ASP* 2.6 39.8 + - - +
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Residues in contact with ALA 12 (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 MET 2.9 19.5 + - - +
9A ALA* 4.0 7.9 - - - +
10A ALA 3.4 0.2 - - - -
11A SER* 1.3 76.1 - - - +
13A ASP* 1.3 60.6 + - - +
15A ASP* 3.1 11.4 + - - +
16A ALA* 2.9 27.7 + - - +
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Residues in contact with ASP 13 (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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9A ALA* 2.7 26.3 + - - +
10A ALA* 3.6 7.0 - - - +
11A SER 3.1 0.6 - - - -
12A ALA* 1.3 79.1 - - - +
14A GLU* 1.3 59.4 + - - +
16A ALA* 3.1 1.6 + - - -
17A CYS* 2.9 24.9 + - - +
110B LYS* 2.6 38.7 + - - -
111B PHE* 3.0 23.3 - - + -
350B TYR* 3.6 9.6 - - - +
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Residues in contact with GLU 14 (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 3.1 11.7 + - - +
11A SER* 3.8 10.6 + - - +
13A ASP* 1.3 76.6 - - - +
15A ASP* 1.3 63.3 + - - +
17A CYS* 3.6 2.0 - - - +
18A MET* 2.9 44.7 + - + +
348B TYR* 2.7 40.5 + - - -
350B TYR* 3.2 36.7 + - + -
351B ALA* 3.0 18.2 + - + +
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Residues in contact with ASP 15 (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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11A SER* 2.6 34.2 + - - +
12A ALA* 3.2 13.5 - - - +
14A GLU* 1.3 84.2 - - - +
16A ALA* 1.3 55.9 + - - +
18A MET* 3.6 9.6 + - - +
19A PHE* 3.2 26.0 + - - +
305B PRO* 5.0 4.5 - - - +
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Residues in contact with ALA 16 (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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12A ALA 2.9 12.8 + - - +
13A ASP* 3.6 2.9 - - - +
15A ASP* 1.3 74.7 - - - +
17A CYS* 1.3 58.6 + - - +
19A PHE* 3.5 6.2 + - - -
20A ALA* 3.0 24.4 + - - +
107B PRO* 4.5 11.7 - - + -
108B VAL* 3.5 23.4 - - + +
111B PHE* 3.3 29.3 - - + -
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Residues in contact with CYS 17 (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 ASP 2.9 16.2 + - - +
14A GLU* 3.6 9.2 - - - +
15A ASP 3.3 0.2 - - - -
16A ALA* 1.3 77.2 - - - +
18A MET* 1.3 57.3 + - - +
20A ALA* 3.2 4.7 + - - +
21A LEU* 2.9 27.3 + - - +
111B PHE* 3.3 28.4 - - + -
121B MET* 4.0 26.1 - - - +
183B ILE* 5.3 3.6 - - - -
350B TYR* 4.1 13.2 - - + -
351B ALA* 3.9 23.8 - - + -
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Residues in contact with MET 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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14A GLU* 2.9 28.4 + - - +
15A ASP* 3.9 9.0 - - - +
17A CYS* 1.3 73.0 - - - +
19A PHE* 1.3 55.0 + - - +
21A LEU* 3.1 11.6 + - + +
22A GLN* 2.8 34.3 + - - +
305B PRO* 3.7 20.0 - - + +
306B SER* 3.4 18.8 - - - +
348B TYR* 4.1 5.6 - - - +
351B ALA* 3.5 13.0 - - + -
352B ASN* 2.8 63.3 - - - +
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Residues in contact with PHE 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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15A ASP 3.2 15.1 + - - +
16A ALA* 3.7 6.5 - - - +
17A CYS 3.3 0.2 - - - -
18A MET* 1.3 78.4 - - - +
20A ALA* 1.3 57.3 + - - +
22A GLN* 3.2 21.1 + - - +
23A LEU* 2.9 64.9 + - + +
84B TYR* 3.5 21.5 - - + -
85B ASN* 4.1 15.0 - - + -
86B VAL* 4.8 0.2 - - + -
108B VAL* 3.3 33.7 - - + -
305B PRO* 3.8 18.5 - - + +
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Residues in contact with ALA 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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16A ALA 3.0 15.4 + - - +
17A CYS 3.4 9.2 - - - +
18A MET 3.2 0.2 - - - -
19A PHE* 1.3 78.1 - - - +
21A LEU* 1.3 56.2 + - - +
23A LEU* 3.2 5.8 + - - +
24A ALA* 2.9 28.1 + - - +
108B VAL* 3.6 15.8 - - + +
111B PHE* 3.6 24.5 - - + +
112B LEU* 3.7 20.9 - - + +
121B MET* 4.2 5.6 - - + -
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Residues in contact with LEU 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 CYS* 2.9 17.1 + - - +
18A MET* 3.1 12.5 + - + +
20A ALA* 1.3 75.1 - - - +
22A GLN* 1.3 65.4 + - - +
24A ALA* 3.1 15.3 + - + +
25A SER* 3.3 15.1 + - - -
121B MET* 3.4 32.3 - - + -
124B LEU* 3.6 20.6 - - + -
180B HIS* 4.2 14.6 - - + +
184B ILE* 6.2 0.2 - - + -
263B TRP* 5.8 1.1 - - + -
351B ALA* 4.0 32.8 - - + +
352B ASN* 6.1 2.0 - - - +
602B CIY 5.3 4.5 - - - +
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Residues in contact with GLN 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 MET 2.8 18.8 + - - +
19A PHE* 3.2 28.5 + - - +
21A LEU* 1.3 73.3 - - - +
23A LEU* 1.3 63.3 + - + +
25A SER* 3.4 8.1 + - - -
26A SER* 3.2 20.0 + - - -
84A TYR* 3.1 18.0 + - - +
305B PRO* 3.9 27.1 - - + +
308B GLN* 2.8 32.7 + - + +
309B GLY* 5.5 5.1 - - - -
312B HIS* 3.5 22.7 - - + +
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Residues in contact with LEU 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 PHE* 2.9 62.6 + - + +
20A ALA* 3.5 4.7 - - - +
22A GLN* 1.3 76.2 - - + +
24A ALA* 1.3 60.7 + - - +
25A SER 3.0 4.9 - - - -
26A SER* 2.9 24.5 + - - +
29B LEU* 4.2 25.8 - - + -
30B PRO* 5.0 0.5 - - - +
33B LEU* 3.7 26.8 - - + +
84B TYR* 5.8 0.4 - - + -
86B VAL* 4.1 18.4 - - + -
108B VAL* 3.9 14.8 - - + -
112B LEU* 4.1 15.7 - - + -
125B ALA* 5.1 0.2 - - - +
129B GLN* 4.6 3.5 + - - -
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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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20A ALA 2.9 16.7 + - - +
21A LEU* 3.1 10.7 + - - +
23A LEU* 1.3 75.4 - - - +
25A SER* 1.3 58.0 + - - +
26A SER 3.7 0.4 - - - -
33B LEU* 4.9 0.2 - - - +
112B LEU* 5.6 1.1 - - + +
121B MET* 3.6 22.9 - - + +
124B LEU* 3.9 11.7 - - + -
125B ALA* 3.4 25.5 - - + +
128B ASN* 3.1 12.9 + - - +
129B GLN* 2.9 20.5 + - - -
602B CIY 5.4 0.9 - - - +
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Residues in contact with SER 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 LEU 3.3 12.4 + - - -
22A GLN* 3.4 2.2 - - - -
23A LEU 3.0 0.4 - - - -
24A ALA* 1.3 80.5 - - - +
26A SER* 1.3 56.5 + - - +
27A SER* 3.2 7.2 + - - -
28A VAL* 3.3 11.3 - - - +
128B ASN* 3.8 8.5 - - - +
129B GLN* 4.1 4.5 - - - -
312B HIS* 2.7 42.6 + - - +
313B VAL* 5.9 0.5 - - - +
316B ILE* 3.7 28.7 - - - -
602B CIY 3.9 5.3 + - - -
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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