Contacts of the helix formed by residues 16 - 25 (chain A) in PDB entry 1P3W
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 16 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14A PRO 3.4 2.5 + - - -
15A VAL* 1.3 73.2 - - - +
17A PRO* 1.3 77.0 - - - +
18A ARG* 2.8 57.8 + - - +
19A VAL* 2.9 28.3 + - + -
20A ALA* 2.9 10.4 + - - +
208A TYR* 3.0 12.2 + - + +
258A ILE* 4.1 5.4 - - - -
359A ARG* 2.6 40.2 + - - +
360A PHE* 4.8 5.7 - - + -
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Residues in contact with PRO 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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15A VAL 3.5 4.0 - - - +
16A ASP* 1.3 92.3 - - - +
18A ARG* 1.3 58.6 + - + +
20A ALA* 3.2 3.2 + - + +
21A GLU* 2.9 31.8 + - - +
360A PHE* 4.6 15.3 - - + -
28B THR* 4.2 20.6 - - + -
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Residues in contact with ARG 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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16A ASP* 2.8 34.7 + - - +
17A PRO* 1.3 76.9 - - + +
19A VAL* 1.3 64.7 + - - +
21A GLU* 3.1 34.4 - - - +
22A LYS* 3.2 16.8 + - - +
254A GLU* 4.0 9.0 - - - +
257A ARG* 5.0 6.8 - - - +
258A ILE* 3.5 38.1 - - + +
262A GLU* 2.7 32.9 + - - +
359A ARG* 4.4 2.4 - - - +
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Residues in contact with VAL 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* 3.6 16.2 - - + -
16A ASP* 2.9 25.8 + - + +
18A ARG* 1.3 75.7 - - - +
20A ALA* 1.3 65.1 + - - +
22A LYS* 3.2 3.8 + - - +
23A MET* 3.0 28.5 + - - +
208A TYR 3.8 7.4 - - - +
210A PRO* 4.2 6.3 - - + -
251A GLY* 3.3 30.3 - - - +
254A GLU* 3.7 12.1 - - + -
255A ALA* 3.7 31.4 - - - +
258A ILE* 4.0 3.8 - - + -
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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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15A VAL* 3.7 14.1 - - + +
16A ASP 2.9 11.2 + - - +
17A PRO* 3.5 7.4 - - + +
19A VAL* 1.3 77.6 - - - +
21A GLU* 1.3 62.0 + - - +
23A MET* 3.3 1.8 + - - +
24A MET* 2.8 46.1 + - + +
27B MET* 4.2 15.7 - - + -
28B THR* 4.1 17.9 - - + -
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Residues in contact with GLU 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 PRO 2.9 15.3 + - - +
18A ARG* 3.1 37.4 - - - +
20A ALA* 1.3 76.5 - - - +
22A LYS* 1.3 75.1 + - + +
24A MET* 3.5 18.8 + - - +
25A GLN* 3.5 18.3 + - - +
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Residues in contact with LYS 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 ARG* 3.2 15.5 + - - +
19A VAL 3.2 8.4 + - - +
21A GLU* 1.3 89.7 + - + +
23A MET* 1.3 63.5 + - + +
25A GLN* 3.0 37.6 + - - +
26A PHE* 3.2 15.9 - - + -
250A VAL* 4.0 19.3 - - + +
254A GLU* 3.9 31.8 + - + +
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Residues in contact with MET 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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15A VAL* 4.7 0.4 - - - -
19A VAL* 3.0 26.5 + - - +
20A ALA* 3.6 7.9 - - - +
22A LYS* 1.3 76.3 - - - +
24A MET* 1.3 57.5 + - - +
26A PHE* 3.0 21.7 + - - +
27A MET* 3.6 16.7 - - - +
210A PRO* 3.7 25.6 - - + -
247A HIS* 3.3 42.8 - - + +
248A GLN* 3.3 25.8 - - - +
250A VAL* 4.4 1.5 - - - +
251A GLY* 3.4 11.2 - - - -
27B MET* 3.6 31.6 - - + -
247B HIS* 4.1 4.3 - - + +
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Residues in contact with MET 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* 2.8 49.7 + - + +
21A GLU* 3.6 15.7 - - - +
22A LYS 3.2 0.4 - - - -
23A MET* 1.3 77.8 - - - +
25A GLN* 1.3 59.8 + - + +
26A PHE 3.1 1.8 + - - -
27A MET* 3.9 18.2 + - - +
28A THR* 4.8 6.8 + - - +
24B MET* 3.2 55.1 - - + +
27B MET* 4.8 4.5 - - - -
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Residues in contact with GLN 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 GLU* 3.5 13.8 + - - +
22A LYS* 3.0 38.0 + - - +
24A MET* 1.3 76.8 - - + +
26A PHE* 1.3 75.6 + - + +
27A MET 3.6 0.9 - - - -
31A GLY* 3.5 8.5 - - - -
32A THR* 3.0 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