Contacts of the helix formed by residues 9 - 23 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6B LEU* 3.2 15.6 + - - +
8B GLY* 1.3 75.8 - - - +
10B ALA* 1.3 63.1 + - - +
11B PRO* 3.2 12.6 - - - +
12B CYS* 3.3 20.9 - - - +
13B ARG* 3.0 23.6 + - - +
52B ILE* 4.4 6.5 + - - -
302B GTX 3.1 41.0 - - - +
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Residues in contact with ALA 10 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8B GLY 3.5 0.8 + - - -
9B SER* 1.3 70.2 - - - +
11B PRO* 1.3 75.3 - - + +
13B ARG* 3.0 17.9 + - - +
14B ALA* 2.9 19.1 + - - +
105B TYR* 3.8 24.0 + - + -
161B ALA* 3.4 32.7 - - + +
162B THR* 4.2 3.1 - - - +
165B THR* 3.6 11.4 - - + +
302B GTX 5.5 0.6 - - - +
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Residues in contact with PRO 11 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9B SER* 3.2 16.4 - - - +
10B ALA* 1.3 93.7 - - + +
12B CYS* 1.3 59.1 + - - +
14B ALA* 3.2 16.4 + - + +
15B VAL* 3.3 10.4 + - - +
53B PRO* 3.8 8.3 - - + -
65B SER* 3.4 35.7 - - - +
66B ARG* 5.2 8.1 - - - +
105B TYR* 4.3 19.3 - - + +
302B GTX 3.8 34.3 - - + +
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Residues in contact with CYS 12 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3B PHE* 3.5 2.3 - - + -
5B TYR* 3.5 38.8 - - + -
6B LEU 3.7 12.6 - - - +
9B SER* 3.2 28.8 + - - +
10B ALA 3.2 0.8 - - - -
11B PRO* 1.3 77.6 - - - +
13B ARG* 1.3 63.4 + - - +
15B VAL* 3.0 14.6 + - - +
16B GLN* 3.1 17.4 + - - +
52B ILE* 4.0 5.8 - - - -
53B PRO* 3.5 31.9 - - - -
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Residues in contact with ARG 13 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7B PRO 2.9 29.0 + - - +
8B GLY 3.1 21.0 + - - -
9B SER 3.0 7.7 + - - +
10B ALA* 3.0 20.3 + - - +
12B CYS* 1.3 77.5 - - - +
14B ALA* 1.3 63.7 + - - +
16B GLN* 3.2 20.2 + - - +
17B MET* 3.1 29.2 + - - +
161B ALA* 2.8 27.2 + - + +
164B ALA* 4.1 6.9 - - - +
165B THR* 2.8 26.7 + - - +
195B LEU 4.1 2.9 - - - +
196B ASN* 2.8 56.4 + - - +
199B GLY* 3.8 1.6 - - - -
200B ALA* 3.6 17.2 - - - +
203B PHE* 4.8 0.4 - - - +
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Residues in contact with ALA 14 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10B ALA 2.9 11.8 + - - +
11B PRO* 3.3 14.8 - - + +
12B CYS 3.1 0.2 - - - -
13B ARG* 1.3 76.6 - - - +
15B VAL* 1.3 60.3 + - - +
17B MET* 3.5 4.3 + - - +
18B THR* 2.9 27.9 + - - -
65B SER* 4.9 2.5 - - - +
69B GLN* 3.9 23.1 - - - +
157B LEU* 4.2 6.5 - - - +
158B SER* 3.9 19.7 - - - +
161B ALA* 3.8 10.0 - - + +
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Residues in contact with VAL 15 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3B PHE* 3.7 21.5 - - + -
11B PRO 3.6 13.2 - - - +
12B CYS 3.0 7.9 + - - +
14B ALA* 1.3 76.3 - - - +
16B GLN* 1.3 58.0 + - - +
18B THR* 3.1 6.5 + - - -
19B ALA* 2.9 27.2 + - - +
26B LEU* 4.3 8.5 - - + -
53B PRO* 3.9 17.9 - - + -
55B LEU* 5.8 0.2 - - + -
65B SER* 3.8 23.1 - - - +
68B ILE* 3.6 28.5 - - + -
69B GLN* 4.5 2.5 - - + -
72B LEU* 3.9 11.2 - - + -
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Residues in contact with GLN 16 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3B PHE* 3.5 15.7 - - + -
5B TYR* 3.4 38.4 + - - -
7B PRO* 4.6 4.4 - - - +
12B CYS 3.1 9.9 + - - +
13B ARG* 3.2 30.4 + - - +
15B VAL* 1.3 76.4 - - - +
17B MET* 1.3 61.5 + - - +
19B ALA* 3.4 2.6 + - - +
20B ALA* 3.0 23.6 + - - +
26B LEU* 4.2 12.6 - - + -
28B LEU* 4.1 13.5 - - - +
195B LEU* 4.3 45.0 + - + +
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Residues in contact with MET 17 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13B ARG 3.1 19.8 + - - +
14B ALA* 3.9 3.8 - - - +
16B GLN* 1.3 76.2 - - + +
18B THR* 1.3 58.4 + - - +
20B ALA* 3.3 2.2 + - - -
21B ALA* 2.9 27.5 + - - +
157B LEU* 3.2 51.0 - - + +
160B ALA* 4.5 2.0 - - - -
161B ALA* 3.8 10.1 - - + +
190B ALA* 4.3 2.5 - - - -
191B PRO 3.3 25.6 - - - +
192B GLY* 3.6 15.3 - - - +
193B TYR* 4.1 19.3 - - - -
195B LEU* 5.7 0.2 - - + -
196B ASN* 3.6 38.8 - - + +
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Residues in contact with THR 18 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14B ALA 2.9 17.4 + - - -
15B VAL* 3.1 6.4 + - - -
17B MET* 1.3 78.3 - - - +
19B ALA* 1.3 55.6 + - - +
21B ALA* 3.2 3.7 + - - +
22B VAL* 3.0 33.1 + - + +
69B GLN* 3.0 49.9 + - - +
72B LEU* 4.3 11.4 - - + -
73B ALA 4.8 0.2 - - - +
82B LEU* 5.0 1.1 - - + -
154B ILE* 3.8 17.9 - - + +
157B LEU* 3.5 15.4 - - + +
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Residues in contact with ALA 19 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15B VAL 2.9 16.5 + - - +
16B GLN 3.8 2.7 - - - +
18B THR* 1.3 74.2 - - - +
20B ALA* 1.3 65.6 + - - +
22B VAL* 3.2 3.7 + - - +
23B GLY 2.9 19.8 + - - -
24B VAL* 3.0 33.1 + - + +
26B LEU* 3.8 30.1 - - + -
72B LEU* 4.2 12.5 - - + +
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Residues in contact with ALA 20 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16B GLN 3.0 14.3 + - - +
17B MET 3.4 9.0 - - - +
19B ALA* 1.3 77.5 - - - +
21B ALA* 1.3 62.2 + - - +
23B GLY* 3.4 10.2 + - - -
24B VAL 5.1 1.1 - - - -
191B PRO* 3.8 4.9 - - + +
192B GLY* 3.8 29.2 - - - +
195B LEU* 5.4 4.3 - - + -
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Residues in contact with ALA 21 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17B MET 2.9 17.7 + - - +
18B THR* 3.4 5.6 - - - +
19B ALA 3.1 0.2 - - - -
20B ALA* 1.3 78.5 - - - +
22B VAL* 1.3 59.1 + - - +
23B GLY 3.4 0.4 + - - -
78B LYS* 5.8 3.8 - - - +
82B LEU* 3.3 33.9 - - + +
157B LEU* 4.3 3.8 - - + -
191B PRO* 3.6 24.9 - - + +
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Residues in contact with VAL 22 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18B THR* 3.0 20.3 + - + +
19B ALA* 3.2 4.2 + - - +
21B ALA* 1.3 79.0 - - - +
23B GLY* 1.3 61.8 + - - +
24B VAL* 3.6 8.0 - - + +
72B LEU* 3.7 17.5 - - + +
73B ALA* 4.0 15.3 - - - +
76B TYR* 3.1 52.1 - - + +
77B GLY* 3.3 8.5 - - - +
78B LYS* 5.7 8.9 + - - +
82B LEU* 4.0 13.5 - - + -
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Residues in contact with GLY 23 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19B ALA 2.9 5.4 + - - -
20B ALA 3.4 10.4 + - - -
21B ALA 3.4 0.4 - - - -
22B VAL* 1.3 81.7 - - - +
24B VAL* 1.3 61.8 + - - +
25B GLU 4.2 0.7 + - - -
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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