Contacts of the helix formed by residues 57 - 65 (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 SER 57 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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56E VAL* 1.3 77.7 - - - +
58E PRO* 1.3 72.8 - - - +
59E ALA* 3.1 8.1 + - - +
60E THR* 2.7 41.6 + - - +
61E VAL* 3.5 12.3 + - - +
96E TRP* 4.0 0.7 - - - -
563E ALA* 3.6 18.4 - - - +
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Residues in contact with PRO 58 (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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56E VAL 4.4 0.2 - - - +
57E SER* 1.3 83.5 - - - +
59E ALA* 1.3 56.6 + - - +
61E VAL* 2.9 2.6 + - - +
62E ILE* 2.9 38.0 + - + +
95E PRO* 4.4 21.5 - - + +
96E TRP* 3.5 50.7 - - + +
99E ALA* 4.0 20.6 - - + -
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Residues in contact with ALA 59 (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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57E SER* 3.1 6.2 + - - +
58E PRO* 1.3 79.5 - - - +
60E THR* 1.3 64.7 - - + +
62E ILE* 3.4 7.3 + - - +
63E ARG* 3.0 41.1 + - - +
99E ALA* 5.4 1.5 - - - +
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Residues in contact with THR 60 (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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154D GLU* 4.4 15.9 + - - +
159D PHE* 5.3 1.8 - - - -
56E VAL* 3.4 19.0 - - + +
57E SER* 2.7 33.2 + - - +
59E ALA* 1.3 77.3 - - + +
61E VAL* 1.3 60.0 + - - +
63E ARG* 3.4 26.6 + - - +
64E ARG* 3.5 21.3 + - - +
562E VAL* 5.3 2.7 - - + +
563E ALA* 6.2 1.3 - - + -
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Residues in contact with VAL 61 (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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159D PHE* 4.0 23.8 - - + -
48E VAL* 4.4 12.1 - - + -
50E ILE* 4.2 15.5 - - + -
56E VAL* 4.0 18.4 - - + -
57E SER 3.6 14.8 - - - +
58E PRO 2.9 9.8 + - - +
60E THR* 1.3 74.5 - - - +
62E ILE* 1.3 69.8 + - + +
64E ARG* 3.3 1.3 + - - +
65E PHE* 2.9 27.0 + - + +
68E VAL* 5.5 0.2 - - + -
71E VAL* 6.0 2.5 - - + -
96E TRP* 3.9 23.1 - - + -
104E TYR* 3.6 17.7 + - + +
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Residues in contact with ILE 62 (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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58E PRO* 2.9 29.2 + - + +
59E ALA* 4.1 5.2 - - - +
61E VAL* 1.3 82.5 - - + +
63E ARG* 1.3 60.7 + - - +
64E ARG 3.5 0.2 + - - -
65E PHE 3.7 13.3 + - - -
66E PRO* 3.7 7.6 - - + +
96E TRP* 5.9 0.9 - - + -
99E ALA* 3.2 42.4 - - + +
100E MET* 4.3 5.4 - - + +
103E SER* 3.2 36.6 - - - +
104E TYR* 3.5 32.5 - - + +
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Residues in contact with ARG 63 (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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42E ARG* 3.1 21.1 + - - +
59E ALA* 3.0 28.2 + - - +
60E THR* 3.4 37.2 + - - +
62E ILE* 1.3 79.3 - - - +
64E ARG* 1.3 62.4 + - - +
66E PRO* 4.0 5.0 - - - +
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Residues in contact with ARG 64 (chain E).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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151D VAL* 4.1 4.9 - - - +
154D GLU* 2.9 38.2 + - - +
155D ASN* 3.0 29.2 + - - -
159D PHE* 3.8 8.0 - - + -
31E SER* 3.6 18.2 - - - -
38E TYR* 3.3 43.5 + - - +
41E GLU* 4.3 2.4 + - - -
42E ARG* 2.8 44.0 + - + +
45E ARG* 4.3 1.0 - - - +
60E THR 3.5 13.1 + - - +
61E VAL* 3.3 3.2 + - - +
63E ARG* 1.3 84.1 - - + +
65E PHE* 1.3 92.7 + - + +
66E PRO* 3.1 5.4 - - - +
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Residues in contact with PHE 65 (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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159D PHE* 3.5 39.0 - + - -
41E GLU* 3.7 10.3 - - - -
42E ARG* 3.7 19.3 - - - +
45E ARG* 3.1 46.0 - - + -
48E VAL* 3.5 19.1 - - + -
61E VAL* 2.9 13.8 + - + +
62E ILE 3.7 1.8 - - - -
64E ARG* 1.3 118.5 - - + +
66E PRO* 1.3 67.5 - - - +
67E LYS 3.0 3.1 + - - +
68E VAL* 3.3 18.9 - - + +
104E TYR* 2.6 26.8 + - - +
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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