Contacts of the helix formed by residues 7 - 27 (chain A) in PDB entry 1P4X
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 7 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3A TYR* 2.6 32.5 + - - -
5A ASN* 3.4 6.5 + - + +
6A HIS* 1.3 74.5 - - - +
8A LYS* 1.3 63.1 + - - +
9A ILE* 3.2 3.5 + - - +
10A ARG* 2.9 28.6 + - - +
11A ASP* 3.3 13.8 + - - +
232A LEU* 5.5 0.5 - - - +
236A ASN* 2.8 33.0 - - - +
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Residues in contact with LYS 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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7A ASP* 1.3 73.7 - - - +
9A ILE* 1.3 64.0 + - - +
10A ARG 3.2 0.2 - - - -
11A ASP* 3.1 11.1 + - - +
12A PHE 3.0 11.8 + - - -
142A TYR* 2.7 30.1 + - - +
236A ASN* 3.6 13.1 - - - +
239A LEU* 2.8 42.4 + - + +
240A ALA* 4.7 3.1 - - - +
241A ASP* 3.6 17.1 - - - +
242A LYS 4.0 7.5 - - - +
243A ASP 4.6 1.2 - - - +
244A HIS* 3.3 45.3 + - + +
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Residues in contact with ILE 9 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A TYR* 4.2 6.1 - - + +
7A ASP* 3.2 11.2 + - - +
8A LYS* 1.3 73.6 - - - +
10A ARG* 1.3 65.8 + - - +
12A PHE* 3.1 3.8 + - - +
13A ILE* 3.0 39.4 + - + +
146A PHE* 4.3 14.4 - - + -
161A PHE* 4.1 28.5 - - + -
162A THR* 6.3 0.2 - - - -
165A ALA* 4.2 10.3 - - + -
232A LEU* 3.6 40.2 - - + +
235A VAL* 4.2 15.9 - - + -
236A ASN* 3.3 20.2 - - - +
239A LEU* 4.7 0.4 - - + -
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Residues in contact with ARG 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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2A LYS* 4.6 12.5 - - - +
3A TYR* 3.3 32.7 + - + +
5A ASN 2.9 30.3 - - - +
6A HIS* 3.3 35.8 + - - +
7A ASP* 2.9 14.5 + - - +
8A LYS 3.2 0.2 - - - -
9A ILE* 1.3 77.2 - - - +
11A ASP* 1.3 66.4 + - - +
13A ILE* 3.4 5.4 + - + +
14A ILE* 3.0 52.4 + - + +
126A SER* 3.8 11.3 + - - -
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Residues in contact with ASP 11 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A ASP 3.3 9.5 + - - +
8A LYS* 3.1 14.2 + - - +
9A ILE 3.1 0.2 - - - -
10A ARG* 1.3 84.3 + - - +
12A PHE* 1.3 64.1 + - - +
14A ILE* 3.3 1.0 + - - +
15A ILE* 2.9 31.3 + - + +
128A MET* 3.2 43.6 - - - +
142A TYR* 3.9 11.7 - - + -
244A HIS* 2.9 26.6 + - + +
245A LEU* 4.5 3.1 - - + +
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Residues in contact with PHE 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 LYS 3.0 4.6 + - - +
9A ILE 3.1 6.3 + - - +
11A ASP* 1.3 79.1 - - - +
13A ILE* 1.3 65.3 + - + +
15A ILE* 3.2 2.0 + - - -
16A GLU* 2.7 68.6 + - + +
142A TYR* 3.5 12.5 - + + -
143A THR* 3.6 28.5 - - - -
146A PHE* 3.3 67.8 - + + -
147A LYS* 4.0 5.2 - - + -
158A PHE* 3.9 23.3 - + - -
162A THR* 4.0 18.2 - - - -
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Residues in contact with ILE 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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3A TYR* 3.9 32.8 - - + -
9A ILE* 3.0 32.7 + - + +
10A ARG* 3.7 4.7 - - - +
12A PHE* 1.3 86.5 - - + +
14A ILE* 1.3 65.1 + - + +
16A GLU* 3.8 3.6 - - - +
17A ALA* 3.1 26.2 + - + +
162A THR* 4.4 24.9 - - + +
165A ALA* 4.4 8.3 - - + -
166A ILE* 4.5 16.2 - - + -
185A HIS* 5.3 1.7 - - + -
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Residues in contact with ILE 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 ARG* 3.0 65.2 + - + +
11A ASP* 3.7 3.4 - - - +
13A ILE* 1.3 79.6 - - + +
15A ILE* 1.3 58.9 + - - +
17A ALA* 3.6 5.1 - - - +
18A TYR* 2.9 29.5 + - + +
21A ARG* 5.2 0.7 + - - -
126A SER* 3.7 20.4 - - - +
128A MET* 3.8 30.3 - - + -
129A ILE* 5.3 4.0 - - + +
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Residues in contact with ILE 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 ASP 2.9 19.1 + - - +
12A PHE* 3.8 1.8 - - - +
14A ILE* 1.3 72.6 - - - +
16A GLU* 1.3 61.0 + - - +
18A TYR* 3.1 8.8 + - + +
19A MET* 2.8 38.6 + - + +
128A MET* 4.0 26.7 - - + -
129A ILE* 5.7 0.7 - - - +
130A PRO* 5.8 0.4 - - + -
139A LEU* 3.7 53.6 - - + +
142A TYR* 3.9 19.5 - - + -
143A THR* 3.6 22.0 - - + -
245A LEU* 4.0 3.1 - - + -
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Residues in contact with GLU 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 PHE* 2.7 40.0 + - + +
13A ILE* 3.8 4.0 - - - +
15A ILE* 1.3 72.9 - - - +
17A ALA* 1.3 61.3 + - - +
19A MET* 3.3 8.1 + - - +
20A PHE* 3.1 21.3 + - - +
143A THR* 3.4 27.4 + - - +
147A LYS* 3.0 32.5 + - - -
158A PHE* 3.9 13.2 - - + -
185A HIS* 3.8 22.3 + - + -
186A HIS* 5.2 0.4 - - + +
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Residues in contact with ALA 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 ILE* 3.1 20.8 + - + +
14A ILE* 3.6 5.8 - - - +
16A GLU* 1.3 73.5 - - - +
18A TYR* 1.3 66.5 + - - +
20A PHE* 3.2 4.9 + - - +
21A ARG* 3.1 38.9 + - - +
185A HIS* 3.7 29.1 - - + +
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Residues in contact with TYR 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 ILE* 2.9 16.0 + - + +
15A ILE* 3.4 10.5 - - + +
17A ALA* 1.3 76.7 - - - +
19A MET* 1.3 69.4 + - + +
21A ARG* 3.2 28.1 + - - +
22A PHE* 2.9 34.3 + + - +
115A ILE* 4.1 7.4 - - - +
118A PHE* 3.5 24.9 - + - -
119A ASN* 2.7 31.4 + - - -
122A ASP* 4.4 3.1 - - - -
129A ILE* 3.7 29.8 - - + -
130A PRO* 3.3 36.9 + - + +
136A PHE* 4.2 15.8 - + - -
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Residues in contact with MET 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 ILE* 2.8 28.9 + - + +
16A GLU* 3.6 10.1 - - - +
17A ALA 3.3 0.2 - - - -
18A TYR* 1.3 74.7 - - + +
20A PHE* 1.3 60.7 + - - +
22A PHE* 3.6 3.0 - - - +
23A LYS* 2.9 35.7 + - - +
130A PRO* 4.1 15.9 - - + -
136A PHE* 3.5 50.5 - - + +
139A LEU* 4.3 4.7 - - + -
140A MET* 3.6 52.9 - - + +
143A THR* 4.7 4.3 - - + -
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Residues in contact with PHE 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 GLU 3.1 9.8 + - - +
17A ALA 3.2 10.1 + - - +
19A MET* 1.3 77.4 - - - +
21A ARG* 1.3 71.6 + - + +
23A LYS* 3.6 6.4 - - + +
24A LYS* 3.0 53.8 + - + +
185A HIS* 3.5 59.2 - + + -
187A LYS* 5.7 11.2 - - + -
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Residues in contact with ARG 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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14A ILE 5.4 0.4 + - - -
17A ALA* 3.1 30.0 + - - +
18A TYR* 3.6 29.2 - - - +
20A PHE* 1.3 90.0 - - + +
22A PHE* 1.3 63.0 + - - +
24A LYS* 3.4 9.7 + - + +
25A LYS* 3.1 20.1 + - - +
118A PHE* 3.7 15.1 - - + -
122A ASP* 2.9 39.2 + - - +
123A GLN* 5.1 10.6 + - - +
124A SER* 6.1 0.2 - - - +
129A ILE* 5.4 3.4 - - - +
185A HIS* 6.0 1.5 - - + +
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Residues in contact with PHE 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 TYR* 2.9 24.9 + - + +
19A MET* 3.6 9.0 - - - +
21A ARG* 1.3 78.0 - - - +
23A LYS* 1.3 62.7 + - - +
25A LYS 3.8 0.2 - - - -
26A VAL* 2.9 41.6 + - + +
34A ILE* 3.6 29.4 - - + -
111A PHE* 4.0 21.1 - + - -
114A ILE* 4.0 13.2 - - + -
115A ILE* 4.2 16.4 - - + -
118A PHE* 3.6 46.4 - + + -
136A PHE* 3.6 38.1 - + - -
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Residues in contact with LYS 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 MET* 2.9 21.1 + - - +
20A PHE* 3.6 6.3 - - + +
22A PHE* 1.3 75.8 - - - +
24A LYS* 1.3 60.7 + - - +
27A LYS* 2.9 53.4 + - + +
34A ILE* 3.5 39.7 - - + +
140A MET* 4.1 21.1 - - - +
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Residues in contact with LYS 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 PHE* 3.0 40.9 + - + +
21A ARG* 3.4 9.9 - - + +
23A LYS* 1.3 79.1 - - - +
25A LYS* 1.3 59.4 + - + +
28A PRO* 3.2 24.4 - - - +
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Residues in contact with LYS 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 ARG 3.1 13.3 + - - +
22A PHE 4.1 1.6 - - - +
24A LYS* 1.3 81.5 - - + +
26A VAL* 1.3 64.6 + - + +
28A PRO* 3.6 6.8 - - - +
29A GLU* 3.7 18.4 - - + +
118A PHE* 3.8 29.8 - - + +
121A ALA* 3.5 32.3 + - - +
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Residues in contact with VAL 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 PHE* 2.9 51.9 + - + +
23A LYS* 5.1 0.2 - - - -
25A LYS* 1.3 80.0 - - + +
27A LYS* 1.3 67.8 + - - +
28A PRO* 3.2 3.6 - - - -
29A GLU* 2.9 16.7 + - - -
30A VAL* 3.1 30.2 + - + +
34A ILE* 5.2 6.3 - - + -
37A PHE* 5.9 4.3 - - + -
111A PHE* 6.1 1.3 - - + -
114A ILE* 4.2 21.8 - - + -
118A PHE* 4.5 12.6 - - + -
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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 LYS* 2.9 41.8 + - + +
26A VAL* 1.3 74.7 - - - +
28A PRO* 1.3 63.6 - - + +
30A VAL* 3.1 23.3 - - - +
32A MET 6.1 1.1 - - - -
33A THR* 6.5 1.8 - - - -
34A ILE* 5.3 7.5 - - + +
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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