Contacts of the helix formed by residues 9 - 22 (chain A) in PDB entry 1PN9
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 SER 9 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6A LEU* 3.0 15.4 + - - +
8A GLY* 1.3 76.0 - - - +
10A ALA* 1.3 63.4 + - - +
11A PRO* 3.1 24.4 - - - +
12A CYS* 3.0 20.0 + - - +
13A ARG* 2.9 24.0 + - - +
52A ILE* 4.3 9.0 - - - -
301A GTX 3.1 28.1 - - - +
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Residues in contact with ALA 10 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8A GLY 3.5 0.8 + - - -
9A SER* 1.3 69.5 - - - +
11A PRO* 1.3 75.3 - - + +
13A ARG* 2.9 28.8 + - - +
14A ALA 2.9 10.9 + - - -
105A TYR* 3.9 24.1 + - + -
113A TYR* 5.7 0.6 + - - +
161A ALA* 3.3 22.1 - - + +
162A THR* 4.4 3.4 - - - +
165A THR* 3.7 20.9 - - + +
301A GTX 5.1 1.0 - - - +
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Residues in contact with PRO 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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9A SER* 3.1 17.3 - - - +
10A ALA* 1.3 94.5 - - + +
12A CYS* 1.3 60.0 + - - +
14A ALA* 3.3 13.5 + - + +
15A VAL* 3.3 18.7 + - - +
53A PRO* 3.7 9.4 - - + -
65A SER* 3.4 30.2 - - - +
66A ARG* 5.1 7.9 - - - +
105A TYR* 4.3 12.8 - - + +
301A GTX 3.7 40.2 - - + +
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Residues in contact with CYS 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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3A PHE* 3.4 11.0 - - - -
5A TYR* 3.4 38.1 - - + -
6A LEU 3.5 13.2 - - - +
9A SER* 3.0 29.0 + - - +
11A PRO* 1.3 78.6 - - - +
13A ARG* 1.3 61.6 + - - +
15A VAL 3.3 2.3 + - - -
16A GLN* 3.1 20.5 + - - +
52A ILE* 3.9 4.9 - - - -
53A PRO* 3.5 31.9 - - - -
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Residues in contact with ARG 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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7A PRO 2.7 29.5 + - - +
8A GLY 3.0 21.2 + - - -
9A SER 2.9 6.9 + - - +
10A ALA* 2.9 19.7 + - - +
12A CYS* 1.3 75.2 - - - +
14A ALA* 1.3 63.9 + - - +
16A GLN* 3.2 20.3 + - - +
17A MET* 3.0 29.2 + - - +
161A ALA* 2.9 22.4 + - + -
164A ALA* 4.4 4.8 - - - +
165A THR* 2.9 25.7 + - - +
195A LEU 4.1 4.9 - - - +
196A ASN* 2.9 58.2 + - - +
199A GLY* 3.5 9.8 - - - -
200A ALA* 4.0 12.1 - - - +
203A PHE* 5.0 0.6 - - - +
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Residues in contact with ALA 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 2.9 11.8 + - - +
11A PRO* 3.5 13.9 - - + +
12A CYS 3.3 0.2 - - - -
13A ARG* 1.3 76.8 - - - +
15A VAL* 1.3 59.0 + - + +
17A MET* 3.4 4.2 + - - +
18A THR* 2.8 32.4 + - - -
65A SER* 5.0 2.9 - - - +
66A ARG* 6.5 0.2 - - - -
69A GLN* 3.7 14.2 + - + +
157A LEU* 4.0 7.0 - - - +
158A SER* 3.9 27.8 - - - +
161A ALA* 3.7 9.8 - - + +
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Residues in contact with VAL 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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3A PHE* 3.4 25.8 - - + -
11A PRO 3.4 14.4 - - - +
12A CYS 3.4 7.4 - - - +
14A ALA* 1.3 76.2 - - - +
16A GLN* 1.3 59.6 + - - +
18A THR* 3.1 7.1 + - - -
19A ALA* 2.7 29.8 + - - +
26A LEU* 4.5 6.3 - - + -
53A PRO* 3.9 11.2 - - + -
55A LEU* 5.9 0.7 - - + -
65A SER* 3.8 28.9 - - - +
68A ILE* 3.9 23.3 - - + -
69A GLN* 4.4 2.5 - - + -
72A LEU* 4.3 9.6 - - + -
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Residues in contact with GLN 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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3A PHE* 3.6 15.3 - - + -
5A TYR* 3.6 38.3 + - - -
7A PRO* 4.5 3.8 - - - +
12A CYS 3.1 14.8 + - - +
13A ARG* 3.2 28.4 + - - +
15A VAL* 1.3 76.4 - - - +
17A MET* 1.3 61.0 + - - +
19A ALA* 3.5 6.6 + - - +
20A ALA* 3.1 21.8 + - - +
26A LEU* 4.6 6.3 - - + -
28A LEU* 4.2 14.8 - - - +
195A LEU* 4.0 51.2 - - + +
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Residues in contact with MET 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 ARG 3.0 18.9 + - - +
14A ALA* 3.8 3.6 - - - +
16A GLN* 1.3 72.6 - - + +
18A THR* 1.3 61.0 + - - +
20A ALA* 3.0 6.0 + - - +
21A ALA* 2.8 28.4 + - - +
157A LEU* 3.2 48.6 - - + +
160A ALA* 4.2 4.3 - - + -
161A ALA* 3.8 9.4 - - + +
190A ALA* 4.5 2.0 - - - -
191A PRO 3.4 23.0 - - - +
192A GLY 3.6 14.1 - - - +
193A TYR* 3.9 20.4 - - - -
196A ASN* 3.5 41.5 - - + +
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Residues in contact with THR 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 ALA 2.8 10.6 + - - -
15A VAL* 3.5 7.4 - - - -
17A MET* 1.3 77.6 - - - +
19A ALA* 1.3 61.7 + - - +
21A ALA* 3.1 12.2 + - - +
22A VAL* 3.1 16.9 + - + +
69A GLN* 2.7 62.5 + - - +
72A LEU* 4.2 12.6 - - + -
73A ALA 4.9 1.3 - - - +
82A LEU* 5.2 0.2 - - + -
154A ILE* 3.8 18.8 - - + -
157A LEU* 3.5 12.6 - - - +
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Residues in contact with ALA 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 VAL 2.7 20.9 + - - +
16A GLN 3.7 3.4 - - - +
18A THR* 1.3 72.8 - - - +
20A ALA* 1.3 59.9 + - - +
22A VAL* 3.4 9.3 - - - +
23A GLY 3.1 2.9 + - - -
24A VAL* 2.7 45.3 + - + +
26A LEU* 3.6 30.3 - - + -
72A LEU* 3.9 13.0 - - + +
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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 GLN 3.1 12.7 + - - +
17A MET 3.0 9.5 + - - +
19A ALA* 1.3 75.8 - - - +
21A ALA* 1.3 59.4 + - - +
23A GLY* 2.9 19.7 + - - -
24A VAL 5.0 1.1 - - - -
191A PRO* 4.1 4.0 - - + +
192A GLY* 3.9 29.4 - - - +
195A LEU* 5.6 3.4 - - + -
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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
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17A MET 2.8 11.9 + - - +
18A THR* 3.1 13.4 + - - +
20A ALA* 1.3 77.7 - - - +
22A VAL* 1.3 59.0 + - - +
23A GLY 3.7 0.3 + - - -
82A LEU* 3.6 27.2 - - + +
157A LEU* 4.3 7.4 - - + -
191A PRO* 3.6 26.0 - - + +
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Residues in contact with VAL 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 THR* 3.1 16.8 + - + +
19A ALA* 3.4 13.5 - - - +
21A ALA* 1.3 75.7 - - - +
23A GLY* 1.3 60.1 + - - +
24A VAL* 3.4 22.3 + - + +
72A LEU* 3.9 21.3 - - + +
73A ALA* 4.1 5.6 - - - +
76A TYR* 4.0 19.7 - - - +
77A GLY* 3.8 23.3 - - - -
78A LYS 6.0 0.2 - - - +
82A LEU* 3.8 23.6 - - + -
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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