Contacts of the helix formed by residues 51 - 55 (chain A) in PDB entry 4C3I
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 ASP 51 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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30A LYS* 2.8 42.6 + - + +
32A ILE* 4.5 8.7 - - + -
44A PRO* 4.2 4.2 - - - +
45A VAL 4.3 7.9 + - - +
46A SER* 3.8 5.9 + - - -
47A GLY 2.9 16.7 + - - -
48A GLY 3.1 17.3 + - - +
49A LEU 3.5 1.4 + - - -
50A TYR* 1.4 78.6 - - - +
52A LEU* 1.3 69.0 + - - +
53A ALA* 3.1 13.4 + - - +
54A LEU* 3.1 28.4 + - + +
55A GLY 4.0 2.9 - - - +
63A SER* 5.7 0.5 - - - -
365A THR* 4.0 1.2 + - - -
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Residues in contact with LEU 52 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43A HIS* 3.6 30.7 - - + +
44A PRO* 3.8 18.6 - - + +
51A ASP* 1.3 73.9 + - - +
53A ALA* 1.4 58.3 + - - +
54A LEU 3.2 0.2 - - - -
55A GLY* 3.2 23.5 + - - +
57A PHE* 3.4 39.5 - - + +
60A ASN* 3.7 20.0 - - + +
61A LEU 4.1 11.2 - - - +
62A CYS* 3.5 0.3 - - - -
63A SER* 2.9 36.4 + - - +
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Residues in contact with ALA 53 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29A ALA* 3.4 19.7 - - - +
30A LYS* 3.7 33.0 - - + -
51A ASP* 3.1 11.5 + - - +
52A LEU* 1.4 74.9 - - - +
54A LEU* 1.4 56.8 + - - +
55A GLY 3.1 5.3 + - - -
63A SER* 4.0 12.8 - - - +
64A THR* 2.7 30.7 + - - +
75A HIS* 3.6 5.0 - - - +
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Residues in contact with LEU 54 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29A ALA* 4.7 2.9 - - + -
30A LYS* 4.6 5.4 - - + +
32A ILE* 3.8 27.4 - - + -
48A GLY 4.4 0.4 - - - +
49A LEU 3.6 24.2 - - - +
51A ASP* 3.1 10.8 + - + +
53A ALA* 1.4 76.9 - - - +
55A GLY* 1.3 56.6 + - - +
74A GLY* 3.8 1.6 - - - -
75A HIS 3.0 40.5 + - - +
76A GLN 3.9 2.2 - - - +
77A GLY* 3.5 29.2 - - - +
362A VAL* 3.8 19.1 - - + +
363A PRO 4.5 0.7 - - - +
365A THR* 3.3 29.6 + - - +
368A ARG* 4.0 5.4 - - - +
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Residues in contact with GLY 55 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51A ASP 4.0 2.1 - - - +
52A LEU* 3.2 27.9 + - - +
53A ALA 3.1 6.1 + - - -
54A LEU* 1.3 81.0 - - - +
56A ALA* 1.3 65.9 + - - -
57A PHE* 3.5 5.5 + - - +
62A CYS* 3.8 12.8 - - - -
72A CYS* 3.8 10.3 - - - -
74A GLY* 4.4 2.9 - - - -
75A HIS* 4.1 1.1 - - - -
365A THR* 4.5 5.0 + - - -
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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