Contacts of the helix formed by residues 50 - 57 (chain D) in PDB entry 2PI8
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 50 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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46D ILE 2.7 19.6 + - - +
49D SER* 1.3 80.9 - - - +
51D PRO* 1.3 58.9 - - - +
52D ARG* 3.1 5.8 + - - +
53D LEU* 3.0 40.5 + - - +
54D TYR 3.1 5.5 + - - -
248D SER 4.7 5.3 + - - -
250D VAL* 3.7 22.0 - - - -
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Residues in contact with PRO 51 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122A ARG* 3.9 14.4 - - - +
143A ASP 5.6 0.2 - - - +
144A LYS* 3.3 42.0 - - + +
146A ILE 5.8 2.0 - - - +
46D ILE 4.4 0.2 - - - +
47D ARG 3.6 19.5 - - - +
48D ASN 4.2 6.3 - - - +
49D SER 3.7 5.2 - - - +
50D SER* 1.3 87.1 - - - +
52D ARG* 1.3 60.2 + - + +
54D TYR* 4.0 6.7 - - + +
55D GLY* 3.4 16.3 + - - -
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Residues in contact with ARG 52 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144A LYS* 3.6 37.0 - - + +
50D SER* 3.1 3.0 - - - +
51D PRO* 1.3 79.9 - - + +
53D LEU* 1.3 64.2 + - - +
54D TYR 3.3 0.2 - - - -
55D GLY* 3.6 1.3 + - - -
56D ASN* 2.8 58.8 + - - +
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Residues in contact with LEU 53 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46D ILE* 4.0 14.3 - - + +
50D SER* 3.0 28.8 + - - +
52D ARG* 1.3 76.5 - - - +
54D TYR* 1.3 64.0 + - - +
56D ASN* 3.5 7.0 + - + +
57D GLN* 3.4 24.5 + - + +
61D TYR* 4.8 0.6 - - - +
248D SER* 4.9 4.3 - - - -
250D VAL* 4.7 2.0 - - + -
267D PRO* 3.2 33.2 - - + +
268D GLY* 3.8 15.3 - - - +
296D LEU* 3.8 29.8 - - + -
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Residues in contact with TYR 54 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43D ILE* 4.4 12.6 - - + -
46D ILE* 3.8 22.4 - - - +
47D ARG* 3.0 69.1 + - + -
50D SER 3.1 7.3 + - - +
51D PRO* 4.1 8.1 - - + +
52D ARG 3.3 0.2 - - - -
53D LEU* 1.3 76.0 - - - +
55D GLY* 1.3 54.9 + - - +
57D GLN 3.0 2.4 + - - -
58D SER* 2.7 55.2 + - - -
61D TYR* 3.8 30.3 - + + -
62D ASN* 3.9 17.3 + - - -
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Residues in contact with GLY 55 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51D PRO 3.4 12.7 + - - -
52D ARG* 3.6 4.4 + - - -
53D LEU 3.4 0.6 - - - -
54D TYR* 1.3 81.8 - - - +
56D ASN* 1.3 62.6 + - - +
58D SER* 3.3 18.0 + - - -
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Residues in contact with ASN 56 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52D ARG* 2.8 43.4 + - - +
53D LEU* 3.9 12.1 - - + +
54D TYR 3.1 0.6 - - - -
55D GLY* 1.3 78.6 - - - +
57D GLN* 1.3 78.1 + - + +
58D SER 3.6 0.4 - - - -
59D ASN* 4.2 7.2 - - - +
60D VAL* 5.1 0.3 - - - +
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Residues in contact with GLN 57 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53D LEU* 3.4 13.5 + - + +
54D TYR 3.0 5.0 + - - -
56D ASN* 1.3 96.3 + - + +
58D SER* 1.3 62.6 + - - +
59D ASN* 3.5 4.3 - - - -
60D VAL* 3.3 28.0 + - + +
61D TYR* 3.0 50.2 + - + +
268D GLY* 3.6 25.9 - - - +
269D THR* 5.5 2.6 - - - +
270D THR 5.6 0.7 + - - -
333D LEU 5.5 0.3 - - - +
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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