Contacts of the helix formed by residues 10 - 19 (chain E) 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 PRO 10 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103D LEU* 3.9 20.0 - - + -
106D ASN* 4.0 10.8 - - - +
8E SER 4.7 0.4 - - - -
9E PHE* 1.3 86.0 - - + +
11E GLU* 1.3 70.7 - - + +
12E GLU* 2.7 19.1 + - - +
13E VAL* 2.8 32.5 + - + +
14E LEU 3.2 4.9 + - - -
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Residues in contact with GLU 11 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9E PHE 3.1 4.4 + - - -
10E PRO* 1.3 68.9 - - + +
12E GLU* 1.3 59.8 + - + +
14E LEU* 3.0 6.1 + - - +
15E GLU* 2.9 29.0 + - - +
40E ILE* 3.8 26.6 - - + +
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Residues in contact with GLU 12 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106D ASN* 3.6 33.7 + - - +
10E PRO* 2.7 17.5 + - - +
11E GLU* 1.3 73.8 - - + +
13E VAL* 1.3 60.2 + - - +
15E GLU* 3.8 11.8 - - - +
16E HIS* 3.1 25.5 + - - +
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Residues in contact with VAL 13 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102D ILE* 3.5 33.2 - - + -
103D LEU* 5.5 1.1 - - + -
106D ASN* 3.6 41.7 - - + +
114D LEU* 4.7 6.1 - - + -
118D CYS* 4.4 4.3 - - - -
9E PHE* 3.7 23.6 - - + -
10E PRO* 2.8 17.2 + - + +
12E GLU* 1.3 76.6 - - - +
14E LEU* 1.3 64.6 + - - +
16E HIS* 3.0 5.0 + - - +
17E VAL* 2.8 32.7 + - + +
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Residues in contact with LEU 14 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8E SER* 5.4 3.6 - - - -
9E PHE* 3.1 48.0 - - + +
10E PRO 3.2 3.0 + - - +
11E GLU 3.0 11.2 + - - +
13E VAL* 1.3 72.5 - - - +
15E GLU* 1.3 66.7 + - - +
17E VAL* 2.9 14.6 + - + +
18E PHE* 3.1 35.7 + - + -
36E SER* 5.5 2.9 - - - +
37E TRP* 3.2 50.9 - - + +
40E ILE* 3.8 25.1 - - + -
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Residues in contact with GLU 15 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11E GLU 2.9 14.8 + - - +
12E GLU* 3.8 10.6 - - - +
14E LEU* 1.3 77.4 - - - +
16E HIS* 1.3 65.5 + - - +
18E PHE* 3.3 6.6 - - - +
19E SER* 2.9 22.7 + - - -
40E ILE* 3.7 17.3 - - + +
43E TRP* 5.1 5.0 - - - +
44E CYS* 4.1 25.2 - - + +
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Residues in contact with HIS 16 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111D LYS* 5.4 5.4 - - + -
114D LEU* 4.1 20.7 + - + +
115D ASP* 2.8 30.9 + - - -
118D CYS* 3.3 36.8 - - + -
12E GLU 3.1 14.5 + - - +
13E VAL* 3.0 9.9 + - - +
15E GLU* 1.3 77.6 - - - +
17E VAL* 1.3 63.1 + - - +
19E SER* 2.9 29.0 + - - -
20E PHE* 3.2 30.3 - + - -
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Residues in contact with VAL 17 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102D ILE* 4.6 2.0 - - + -
118D CYS* 3.8 26.7 - - + +
121D VAL* 4.0 25.1 - - + -
122D ALA* 3.7 29.6 - - + +
125D ILE* 4.2 10.8 - - + -
9E PHE* 5.6 3.6 - - + -
13E VAL* 2.8 26.1 + - + +
14E LEU* 2.9 11.1 + - + +
16E HIS* 1.3 75.8 - - - +
18E PHE* 1.3 58.5 + - + +
20E PHE* 2.7 36.3 + - - +
21E ILE* 3.7 4.7 - - + +
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Residues in contact with PHE 18 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125D ILE* 5.1 2.7 - - + -
14E LEU* 3.1 26.3 + - + -
15E GLU 3.3 9.9 - - - +
17E VAL* 1.3 72.7 - - + +
19E SER* 1.3 59.3 + - - +
20E PHE 2.9 7.3 + - - -
21E ILE* 2.9 29.2 + - + +
27E ARG* 3.2 16.3 + - - +
30E VAL* 4.0 18.2 - - + -
37E TRP* 3.6 43.3 - + - -
40E ILE* 3.9 21.8 - - + -
41E GLU* 3.6 41.1 - - + -
44E CYS* 3.7 13.7 - - - -
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Residues in contact with SER 19 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15E GLU* 2.9 16.4 + - - -
16E HIS* 2.9 27.1 + - - -
17E VAL 3.2 1.0 + - - -
18E PHE* 1.3 68.4 - - - +
20E PHE* 1.3 69.5 + - - +
21E ILE 3.1 4.3 + - - -
22E GLN* 4.2 13.0 - - - +
27E ARG* 4.2 5.6 - - - +
44E CYS* 5.2 1.6 - - - -
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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