Contacts of the helix formed by residues 52 - 56 (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 ASN 52 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157A TRP 5.7 0.2 - - - +
50B ILE* 3.6 8.7 - - - +
51B GLY* 1.3 78.2 - - - +
53B CYS* 1.3 56.2 + - - +
54B TYR* 2.9 25.9 - - - +
55B ALA* 2.8 43.4 + - + +
74B LYS 3.7 3.1 + - - -
75B GLY 4.9 7.1 + - - -
89B TRP* 6.2 0.4 - - - -
509B ARG* 4.4 20.4 - - + +
510B SER* 5.7 0.4 - - - -
557B PHE* 5.6 5.2 - - - -
559B TYR* 3.4 37.8 - - - +
560B ARG 4.4 1.2 - - - +
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Residues in contact with CYS 53 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50B ILE* 4.0 4.8 + - - +
51B GLY 4.0 0.2 - - - -
52B ASN* 1.3 71.0 - - - +
54B TYR* 1.4 91.3 + - - +
55B ALA 3.2 0.2 - - - -
56B VAL 3.0 21.0 - - - +
73B LEU* 3.7 28.7 - - + -
74B LYS 2.9 21.1 + - - +
75B GLY* 3.9 14.1 - - - -
91B GLY* 4.5 2.0 - - - -
92B TYR 5.5 0.9 - - - -
96B TRP* 3.5 18.2 + - - +
115B MET* 4.1 17.7 - - + -
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Residues in contact with TYR 54 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52B ASN* 2.9 15.3 - - - +
53B CYS* 1.4 87.1 - - - +
55B ALA* 1.3 60.5 + - - +
56B VAL 3.1 4.6 + - - -
75B GLY 5.8 0.2 - - - -
89B TRP* 3.9 24.7 - + - -
91B GLY* 2.8 32.8 + - - -
92B TYR 3.9 3.7 + - - -
96B TRP* 6.4 0.2 - - - -
534B ASN* 4.6 2.5 + - - +
559B TYR* 3.5 27.7 - + + +
561B THR* 2.8 20.6 + - - +
563B ALA* 4.0 7.9 - - - +
564B GLY 4.7 0.5 - - - +
566B ARG* 3.5 40.7 + - + +
567B PHE 5.7 0.2 - - - -
568B ASP* 2.8 34.0 + - - -
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Residues in contact with ALA 55 (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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157A TRP* 3.6 25.1 - - - +
158A ALA* 4.5 6.5 - - + +
50B ILE* 5.3 0.2 - - + -
52B ASN* 2.8 33.7 + - + +
54B TYR* 1.3 81.7 - - - +
56B VAL* 1.3 60.7 + - + +
560B ARG* 4.1 9.2 - - + +
561B THR* 3.3 10.7 - - - -
562B VAL* 2.8 27.5 + - - +
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Residues in contact with VAL 56 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154A GLU* 5.4 1.3 - - + -
158A ALA* 3.5 27.1 - - + +
159A PHE* 4.8 4.5 - - + -
50B ILE* 4.1 20.2 - - + -
53B CYS 3.0 17.7 + - - +
54B TYR* 3.1 2.1 - - - -
55B ALA* 1.3 79.4 - - - +
57B SER* 1.3 72.7 + - - +
60B THR* 3.5 24.9 - - + +
61B VAL* 3.8 24.0 - - + -
96B TRP* 3.5 6.1 - - + -
562B VAL* 3.9 13.5 - - + -
563B ALA* 3.9 12.1 - - - -
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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