Contacts of the helix formed by residues 53 - 65 (chain C) in PDB entry 4P3E
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 GLU 53 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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51C SER* 4.9 8.9 + - - +
52C LEU* 1.3 71.5 - - - +
54C ILE* 1.3 64.9 + - - +
55C LEU 3.6 1.6 - - - -
56C GLN* 3.4 23.8 + - + +
57C ILE* 3.1 30.5 + - + +
173C LYS* 3.2 34.7 + - + +
177C GLU* 4.4 3.6 - - - +
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Residues in contact with ILE 54 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52C LEU* 3.3 25.7 + - + +
53C GLU* 1.3 70.3 - - - +
55C LEU* 1.3 66.0 + - - +
57C ILE* 3.0 10.1 + - - +
58C ILE* 3.0 28.8 + - + +
120C LEU* 4.0 16.2 - - + -
161C LEU* 4.3 16.2 - - + -
165C CYS* 5.5 0.9 - - - -
174C THR* 4.5 4.0 - - + +
177C GLU* 3.6 17.6 - - + +
178C ALA* 3.4 42.4 - - + +
181C TYR* 3.9 31.6 - - + -
210C TYR* 5.9 0.9 - - - +
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Residues in contact with LEU 55 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53C GLU 3.6 0.2 - - - -
54C ILE* 1.3 73.4 - - - +
56C GLN* 1.3 57.3 + - - +
58C ILE* 3.3 14.1 - - + +
59C LYS* 3.0 51.3 + - + +
177C GLU* 2.9 27.0 + - - +
210C TYR* 3.7 28.7 - - + +
224C LEU* 4.2 10.8 - - + +
225C TYR* 3.4 43.7 - - + +
228C ARG* 4.0 28.9 - - + +
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Residues in contact with GLN 56 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53C GLU* 3.4 28.1 + - + +
54C ILE 3.2 0.8 - - - -
55C LEU* 1.3 76.0 - - - +
57C ILE* 1.3 66.6 + - + +
59C LYS* 3.5 2.1 + - - +
60C GLU* 3.1 45.2 + - - +
177C GLU* 5.1 1.0 + - - +
224C LEU* 3.7 27.5 - - + +
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Residues in contact with ILE 57 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52C LEU* 3.6 32.8 - - + -
53C GLU* 3.1 27.4 + - + +
54C ILE* 3.0 8.4 + - - +
56C GLN* 1.3 74.5 - - + +
58C ILE* 1.3 63.6 + - + +
60C GLU* 3.1 14.0 + - + +
61C SER* 2.8 43.9 + - - +
82C ARG* 4.6 5.2 - - - +
117C LEU* 4.1 24.5 - - + -
120C LEU* 4.4 11.0 - - + -
121C MET* 4.4 5.8 - - + -
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Residues in contact with ILE 58 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54C ILE* 3.0 15.7 + - + +
55C LEU* 3.3 31.9 - - + +
57C ILE* 1.3 75.6 - - + +
59C LYS* 1.3 63.8 - - + +
61C SER* 4.5 0.9 - - - -
62C GLN* 2.8 57.7 + - - +
75C TYR* 4.5 3.1 - - - -
120C LEU* 3.8 25.6 - - + -
121C MET* 5.5 0.9 - - + -
124C GLU* 3.9 19.5 - - + +
181C TYR* 3.7 25.8 - - + -
210C TYR* 5.3 0.9 - - - +
228C ARG* 4.2 13.5 - - - +
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Residues in contact with LYS 59 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55C LEU* 3.0 39.2 + - + +
56C GLN* 4.0 5.8 - - - +
57C ILE 3.2 0.2 - - - -
58C ILE* 1.3 79.0 - - + +
60C GLU* 1.3 58.5 + - - +
62C GLN* 4.1 11.1 + - - +
63C GLN* 3.1 42.9 + - + +
224C LEU* 4.1 31.2 - - + -
227C GLN* 6.0 5.6 - - - +
228C ARG* 3.8 21.9 - - - +
231C GLU* 3.0 26.2 + - - -
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Residues in contact with GLU 60 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56C GLN* 3.1 43.3 + - - +
57C ILE* 3.3 14.7 - - - +
59C LYS* 1.3 77.0 - - - +
61C SER* 1.3 72.6 + - - +
62C GLN 3.3 0.7 - - - -
63C GLN* 4.2 2.9 - - - +
64C GLN* 3.3 25.1 + - - +
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Residues in contact with SER 61 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57C ILE* 2.8 25.3 + - - +
58C ILE* 3.9 1.1 - - - -
60C GLU* 1.3 80.6 - - - +
62C GLN* 1.3 63.7 + - - +
64C GLN* 3.2 10.1 + - - -
65C HIS* 3.2 20.6 + - - -
75C TYR* 3.6 26.9 - - - -
78C TYR* 3.8 16.2 + - - -
82C ARG* 3.7 21.5 + - - -
121C MET* 5.2 4.4 - - - +
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Residues in contact with GLN 62 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58C ILE* 2.8 44.5 + - - +
59C LYS* 4.1 20.9 + - - +
61C SER* 1.3 79.2 - - - +
63C GLN* 1.3 66.9 + - - +
64C GLN 3.4 0.2 + - - -
65C HIS 3.6 4.3 + - - -
66C GLY 3.8 0.3 + - - -
67C LEU* 3.1 49.1 + - + +
75C TYR* 3.5 29.1 - - + -
124C GLU* 3.3 19.4 + - - -
127C TRP* 4.2 13.1 - - - -
228C ARG* 4.4 10.7 + - - +
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Residues in contact with GLN 63 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59C LYS* 3.1 32.8 + - - +
60C GLU* 4.4 3.1 - - - +
61C SER 3.3 0.8 - - - -
62C GLN* 1.3 81.0 - - + +
64C GLN* 1.3 61.7 + - - +
66C GLY 4.4 0.9 + - - -
67C LEU* 4.0 17.7 + - - +
68C ARG* 3.8 55.0 + - - +
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Residues in contact with GLN 64 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119A A 5.6 2.0 + - - -
60C GLU 3.3 17.0 + - - +
61C SER* 3.2 2.2 + - - -
63C GLN* 1.3 80.5 - - - +
65C HIS* 1.3 87.2 + - + +
66C GLY 3.7 1.9 + - - -
68C ARG* 5.9 1.1 - - - +
74C ARG* 4.7 3.5 + - - -
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Residues in contact with HIS 65 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119A A 4.5 6.3 + - - -
120A G 3.9 13.7 - - - -
61C SER* 3.2 16.2 + - - +
62C GLN 3.6 2.7 + - - -
63C GLN 3.5 0.2 - - - -
64C GLN* 1.3 113.5 + - + +
66C GLY* 1.3 55.1 + - - +
67C LEU 3.9 1.3 - - - -
74C ARG* 2.9 47.3 + - - +
75C TYR* 3.1 29.9 + - + -
78C TYR* 3.1 58.8 + + + -
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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