Contacts of the helix formed by residues 12 - 19 (chain B) in PDB entry 2P1N
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 GLU 12 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106A ASN* 4.3 17.3 + - - +
114A LEU* 5.7 1.9 - - - +
10B PRO* 3.5 13.6 + - - +
11B GLU* 1.3 116.4 + - - +
13B VAL* 1.3 60.9 + - + +
15B GLU* 3.6 21.9 - - - +
16B HIS* 3.1 26.0 + - - +
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Residues in contact with VAL 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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102A ILE* 3.1 35.0 - - + -
103A LEU* 5.1 1.6 - - + -
106A ASN* 3.9 37.7 - - + +
114A LEU* 5.1 4.9 - - + -
118A CYS* 4.2 5.2 - - - -
9B PHE* 4.5 11.9 - - + -
10B PRO* 3.1 26.7 + - + +
12B GLU* 1.3 75.7 - - - +
14B LEU* 1.3 54.5 + - - +
16B HIS* 3.3 4.6 + - - +
17B VAL* 2.6 51.2 + - + +
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Residues in contact with LEU 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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137A PHE* 5.8 1.1 - - + -
9B PHE* 3.5 39.5 - - + +
10B PRO 3.1 8.9 + - - +
11B GLU* 4.8 2.2 - - + -
12B GLU 4.5 1.6 - - - +
13B VAL* 1.3 78.8 - - - +
15B GLU* 1.3 61.7 + - - +
17B VAL* 3.1 9.2 + - + +
18B PHE* 2.9 43.3 + - + -
36B SER* 4.9 4.3 - - - +
37B TRP* 3.5 46.7 - - + +
40B ILE* 3.6 31.4 - - + -
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Residues in contact with GLU 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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11B GLU 4.5 6.8 - - - +
12B GLU* 3.6 20.6 - - - +
13B VAL 3.4 0.4 - - - -
14B LEU* 1.3 77.3 - - - +
16B HIS* 1.3 60.4 + - - +
18B PHE* 3.4 6.7 - - - +
19B SER* 2.9 28.2 + - - -
40B ILE* 3.8 16.7 - - + +
43B TRP* 6.0 1.1 - - - +
44B CYS* 4.1 26.0 - - + +
67B LYS* 5.4 8.6 + - - -
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Residues in contact with HIS 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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111A LYS* 6.2 3.8 - - + -
114A LEU* 3.9 21.2 - - + +
115A ASP* 2.6 34.3 + - - -
118A CYS* 3.3 34.8 - - + -
12B GLU 3.1 18.8 + - - +
13B VAL* 3.3 5.1 + - - +
15B GLU* 1.3 80.9 - - - +
17B VAL* 1.3 59.8 + - - +
19B SER* 2.9 29.1 + - - -
20B PHE* 3.2 18.3 - + - -
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Residues in contact with VAL 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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102A ILE* 4.8 2.5 - - + -
118A CYS* 3.6 24.7 - - + -
121A VAL* 4.1 21.1 - - + -
122A ALA* 4.0 28.7 - - + +
125A ILE* 4.8 7.0 - - + -
9B PHE* 5.2 2.2 - - + -
13B VAL* 2.6 42.4 + - + +
14B LEU* 3.1 16.9 + - + +
16B HIS* 1.3 70.4 - - - +
18B PHE* 1.3 68.6 + - + +
20B PHE* 2.8 33.8 + - - +
21B ILE* 3.8 3.1 + - + +
37B TRP* 6.3 1.1 - - + -
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Residues in contact with PHE 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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125A ILE* 5.7 2.5 - - + -
14B LEU* 2.9 28.8 + - + +
15B GLU 3.4 4.9 - - - +
17B VAL* 1.3 78.2 - - + +
19B SER* 1.3 54.8 + - - +
21B ILE* 2.5 41.0 + - + -
27B ARG* 3.3 26.1 + - - +
30B VAL* 3.9 13.5 - - + -
37B TRP* 3.7 47.3 - + - -
40B ILE* 3.6 35.4 - - + -
41B GLU* 3.8 25.8 - - + -
44B CYS* 3.9 7.2 - - - -
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Residues in contact with SER 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 GLU* 2.9 17.2 + - - -
16B HIS* 2.9 26.4 + - - -
17B VAL 3.2 0.6 - - - -
18B PHE* 1.3 71.7 - - - +
20B PHE* 1.3 71.2 + - - +
22B GLN* 3.8 15.0 - - - +
27B ARG* 4.0 7.3 - - - +
44B CYS* 5.3 1.1 - - - -
46B ARG* 4.0 24.8 + - - +
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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