Contacts of the helix formed by residues 8 - 19 (chain A) in PDB entry 2P3L
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 8 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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9A LEU* 1.3 64.3 + - - +
10A GLY 3.8 3.8 + - - -
11A GLU* 2.7 55.4 + - - +
12A LYS* 3.4 10.6 + - - +
186A TYR* 3.5 28.6 + - - +
188A SER* 4.4 14.6 - - - +
191A ILE* 5.9 1.6 - - + -
233A ASN* 5.7 3.1 - - - -
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Residues in contact with LEU 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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8A THR* 1.3 71.5 - - - +
10A GLY* 1.3 56.2 + - - +
12A LYS* 3.2 22.5 + - + +
13A TRP* 2.9 26.2 + - - +
233A ASN* 4.3 35.6 + - + +
236A SER* 3.8 13.5 - - - +
237A ARG* 4.6 14.1 - - + +
240A ILE* 3.4 26.8 - - + +
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Residues in contact with GLY 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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8A THR* 3.2 4.8 + - - -
9A LEU* 1.3 77.6 - - - +
11A GLU* 1.3 52.2 + - - +
13A TRP* 3.2 10.6 + - - +
14A LYS* 2.7 35.7 + - - +
186A TYR* 3.5 27.5 - - - +
216A HIS* 4.5 1.8 - - - -
233A ASN* 5.5 0.4 + - - -
236A SER* 3.6 18.8 + - - -
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Residues in contact with GLU 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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8A THR* 2.7 45.1 + - - +
10A GLY* 1.3 71.6 - - - +
12A LYS* 1.3 59.8 + - - +
14A LYS* 3.4 4.9 + - - +
15A SER* 3.0 30.5 + - - -
154A PRO* 4.7 9.0 - - + +
186A TYR* 3.5 5.3 - - + -
187A MET* 3.6 37.9 - - - +
188A SER* 4.7 4.9 + - - -
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Residues in contact with LYS 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 THR 3.4 6.2 + - - +
9A LEU* 3.2 28.7 + - + +
11A GLU* 1.3 74.8 - - - +
13A TRP* 1.3 65.1 + - - +
15A SER* 3.4 7.1 + - - -
16A ARG* 3.1 36.3 + - + +
240A ILE* 4.6 11.4 - - + -
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Residues in contact with TRP 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 LEU 2.9 13.1 + - - +
10A GLY* 3.3 15.5 - - - +
12A LYS* 1.3 77.1 - - - +
14A LYS* 1.3 83.4 + - + +
16A ARG* 3.2 4.6 + - - +
17A LEU* 2.8 51.5 + - + +
28A TYR* 3.0 20.0 + - - -
157A GLU* 6.0 0.4 - - - -
186A TYR* 4.0 13.7 - + - -
213A ASN 3.3 21.5 - - - -
214A SER 3.9 5.6 - - - -
215A THR* 4.1 0.7 - - - -
216A HIS* 3.7 46.4 - + + -
236A SER* 4.6 3.6 - - - +
239A LEU* 3.5 29.8 - - + +
240A ILE* 3.8 17.9 - - + +
243A PHE* 3.5 29.7 - + - -
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Residues in contact with LYS 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 GLY 2.7 14.5 + - - +
11A GLU* 3.7 7.4 - - - +
12A LYS 3.3 0.2 - - - -
13A TRP* 1.3 90.5 - - + +
15A SER* 1.3 57.4 + - - +
17A LEU* 3.4 6.8 + - + +
18A ASN* 3.0 43.8 + - - +
151A SER 3.0 26.1 + - - -
152A PRO 3.5 13.0 - - - -
154A PRO* 4.0 18.4 - - + -
157A GLU* 3.5 19.8 + - - -
186A TYR* 3.3 23.8 - - + +
214A SER 5.2 1.0 + - - -
1002A G3A 2.8 35.6 + - - +
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Residues in contact with SER 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 GLU 3.0 17.4 + - - -
12A LYS* 3.6 8.1 - - - -
14A LYS* 1.3 76.6 - - - +
16A ARG* 1.3 63.0 + - - +
18A ASN* 3.3 9.6 + - - +
19A ALA* 3.3 20.4 + - - +
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Residues in contact with ARG 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 LYS* 3.1 28.7 + - + +
13A TRP* 3.6 3.6 - - - +
15A SER* 1.3 76.2 + - - +
17A LEU* 1.3 64.6 + - - +
19A ALA* 3.4 13.6 + - + +
20A LEU* 3.2 24.7 + - + +
240A ILE* 4.0 20.0 + - - +
243A PHE* 3.7 50.1 - - + +
244A THR* 5.0 9.9 - - - +
246A ARG* 6.1 0.8 - - - +
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Residues in contact with LEU 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 TRP* 2.8 35.6 + - + +
14A LYS* 3.7 10.1 - - + +
16A ARG* 1.3 75.1 - - - +
18A ASN* 1.3 59.6 + - - +
20A LEU* 3.3 12.1 + - + +
25A PHE* 3.7 28.0 - - + -
28A TYR* 3.7 30.5 - - + -
214A SER* 3.6 18.2 - - - +
243A PHE* 3.7 12.7 - - + -
1002A G3A 2.9 56.0 + - - +
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Residues in contact with ASN 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 LYS* 3.0 29.6 + - - +
15A SER* 3.7 8.7 - - - +
16A ARG 3.3 0.2 - - - -
17A LEU* 1.3 76.0 - - - +
19A ALA* 1.3 58.5 + - - +
20A LEU 3.3 0.9 - - - +
152A PRO* 2.9 33.0 + - - +
154A PRO* 5.4 0.2 - - - +
1002A G3A 2.7 65.2 + - - +
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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 SER 3.3 11.2 + - - +
16A ARG* 3.8 12.3 - - + +
17A LEU 3.2 1.0 - - - -
18A ASN* 1.3 73.2 - - - +
20A LEU* 1.3 67.1 + - + +
21A GLY 3.5 1.7 + - - -
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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