Contacts of the helix formed by residues 51 - 57 (chain D) in PDB entry 2NYM
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 LEU 51 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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20D LEU* 4.4 12.8 - - + -
35D LEU* 3.8 31.6 - - + -
38D ILE* 4.4 10.5 - - + -
39D ALA* 3.5 39.0 - - + +
42D LEU* 3.9 7.8 - - + +
46D ARG 3.9 0.2 + - - -
47D THR* 3.2 24.6 + - + +
50D GLU* 1.3 77.7 - - - +
52D LEU* 1.3 63.3 + - + +
54D PHE* 3.6 5.5 + - + +
55D LEU* 3.1 45.7 + - + +
76D PHE* 4.1 6.5 - - + -
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Residues in contact with LEU 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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47D THR* 3.2 17.5 + - + +
48D ARG* 4.6 3.1 - - - +
51D LEU* 1.3 76.8 - - + +
53D PRO* 1.3 62.7 - - + +
54D PHE 2.8 5.8 + - - -
55D LEU* 2.8 11.5 + - + +
56D THR* 2.5 44.8 + - - +
73D LEU* 4.4 21.3 - - + -
76D PHE* 4.5 14.8 - - + -
80D VAL* 4.3 4.3 - - + -
88D CYS* 2.7 50.3 - - + +
89D LEU* 3.6 16.4 - - + -
92D PRO* 5.1 5.6 - - + -
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Residues in contact with PRO 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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48D ARG 3.6 18.4 - - - +
49D SER* 3.8 18.8 - - - +
50D GLU 3.7 13.5 - - - +
52D LEU* 1.3 93.0 - - + +
54D PHE* 1.3 54.9 + - - -
56D THR* 4.0 8.5 - - - -
57D ASP* 2.9 32.1 - - - +
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Residues in contact with PHE 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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20D LEU* 3.6 44.6 - - + -
21D ARG* 4.3 32.1 - - + -
50D GLU 3.3 19.3 + - - +
51D LEU* 3.8 6.1 - - + +
52D LEU 2.9 0.6 - - - -
53D PRO* 1.3 77.3 - - - +
55D LEU* 1.3 81.8 - - + +
56D THR 3.1 2.1 + - - -
57D ASP* 3.6 2.0 + - - -
58D THR* 2.7 46.2 + - + -
60D TYR* 3.7 22.9 - + - -
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Residues in contact with LEU 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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32D ILE* 3.7 28.9 - - + -
35D LEU* 3.2 31.4 - - + -
51D LEU* 3.1 33.6 + - + +
52D LEU* 2.8 16.2 + - + +
54D PHE* 1.3 97.6 - - + +
56D THR* 1.3 63.3 + - - +
58D THR* 3.8 15.5 - - - +
60D TYR* 4.3 5.5 - - + +
69D LEU* 3.8 25.6 - - + +
73D LEU* 4.7 4.7 - - + -
92D PRO* 4.4 14.0 - - + +
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Residues in contact with THR 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 LEU* 2.5 26.3 + - - +
53D PRO* 4.2 5.8 - - - -
55D LEU* 1.3 77.1 - - - +
57D ASP* 1.3 68.9 + - - +
58D THR 3.2 5.1 + - - +
91D PRO* 3.8 21.9 - - + +
92D PRO* 3.6 28.3 - - - +
95D SER* 5.0 7.8 + - - +
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Residues in contact with ASP 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 PRO* 2.9 23.9 + - - +
54D PHE* 3.6 3.1 + - - +
55D LEU 3.5 0.2 - - - -
56D THR* 1.3 87.0 - - - +
58D THR* 1.3 65.1 + - - +
59D ILE* 4.2 3.3 - - - +
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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