Contacts of the helix formed by residues 60 - 70 (chain C) in PDB entry 4WLU
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 HIS 60 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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33C SER* 3.5 16.2 - - - +
38C GLN* 5.7 1.8 - - - +
59C ALA* 1.3 93.4 - - + +
61C THR* 1.3 63.3 + - - +
62C PRO* 3.3 6.6 - - - +
63C GLY* 3.2 5.9 + - - -
64C VAL* 3.2 24.5 + - + +
81C LEU* 4.0 4.9 - - - +
241D LYS 4.9 3.4 + - - -
244D ALA* 3.9 28.1 - - + +
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Residues in contact with THR 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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32C ALA* 4.5 3.8 - - + -
33C SER* 3.6 7.2 - - - +
55C LEU* 3.6 26.6 - - + +
56C TYR 3.7 4.3 - - - +
57C ASP* 3.5 25.9 + - + +
59C ALA 3.1 3.2 + - - -
60C HIS* 1.3 73.1 - - - +
62C PRO* 1.4 61.2 - - - +
64C VAL* 3.2 5.0 + - + +
65C ALA* 2.9 31.7 + - - +
79C GLY* 4.5 1.8 - - - -
80C TYR 2.8 32.4 + - - +
81C LEU* 3.3 18.9 - - - +
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Residues in contact with PRO 62 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60C HIS* 3.4 5.4 - - - -
61C THR* 1.4 97.8 - - - +
63C GLY* 1.3 55.5 + - - +
65C ALA* 3.9 5.5 - - + +
66C ALA* 3.0 30.2 + - - +
79C GLY* 4.8 9.2 - - - +
81C LEU* 4.2 28.0 - - + -
240D ALA* 4.5 11.3 - - + +
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Residues in contact with GLY 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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60C HIS 3.2 7.9 + - - -
62C PRO* 1.3 76.9 - - - +
64C VAL* 1.3 59.8 + - - +
66C ALA* 3.5 1.7 + - - +
67C ASP* 3.0 28.6 + - - +
237D VAL* 4.5 1.0 - - - +
240D ALA* 3.6 26.7 + - - -
241D LYS* 3.7 26.7 - - - +
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Residues in contact with VAL 64 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32C ALA* 4.3 15.0 - - + +
33C SER* 4.0 12.6 - - - +
38C GLN* 3.7 30.7 - - + +
41C SER* 5.3 0.9 - - - -
55C LEU* 4.0 9.4 - - + -
60C HIS* 3.2 17.1 + - + +
61C THR* 3.6 8.7 - - + +
63C GLY* 1.3 76.1 - - - +
65C ALA* 1.3 58.3 + - - +
67C ASP* 3.3 8.4 - - - +
68C LEU* 3.0 45.0 + - + +
241D LYS* 4.8 6.7 - - - +
249D LEU* 4.0 13.2 - - + -
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Residues in contact with ALA 65 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55C LEU* 4.0 5.6 - - + +
61C THR 2.9 15.5 + - - +
62C PRO* 3.9 4.5 - - + +
64C VAL* 1.3 75.3 - - - +
66C ALA* 1.3 58.9 + - - +
68C LEU* 3.3 0.9 + - - +
69C SER* 2.8 32.7 + - - -
77C VAL* 4.0 18.8 - - + +
78C LYS* 4.0 6.1 - - - -
79C GLY* 3.4 31.6 - - - +
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Residues in contact with ALA 66 (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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62C PRO 3.0 18.3 + - - +
63C GLY 3.8 4.9 - - - +
65C ALA* 1.3 72.1 - - - +
67C ASP* 1.3 66.3 + - - +
69C SER* 2.7 22.7 + - - -
70C HIS* 3.5 14.2 + - - -
236D GLU* 5.3 8.3 - - + +
237D VAL* 4.1 11.4 - - + +
240D ALA* 4.0 20.4 - - + -
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Residues in contact with ASP 67 (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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63C GLY 3.0 15.0 + - - +
64C VAL* 3.3 13.2 - - - +
66C ALA* 1.3 77.8 - - - +
68C LEU* 1.3 61.7 + - + +
70C HIS* 3.4 8.1 + - - +
237D VAL* 4.3 12.7 - - + +
241D LYS* 3.3 10.2 + - - -
247D ALA* 4.0 5.2 - - - -
248D THR* 2.8 37.2 + - - -
249D LEU* 3.0 13.5 + - + +
250D SER* 2.7 55.0 + - - -
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Residues in contact with LEU 68 (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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41C SER* 3.7 32.8 - - - +
42C LEU* 3.8 20.2 - - - -
45C LYS* 3.2 20.1 - - + -
53C LEU* 4.8 2.5 - - + -
55C LEU* 3.7 20.4 - - + -
64C VAL* 3.0 17.6 + - + +
65C ALA 4.0 2.9 - - - +
67C ASP* 1.3 73.6 - - - +
69C SER* 1.3 64.2 + - - +
71C ILE* 3.2 31.0 + - + +
77C VAL* 4.2 13.5 - - + -
249D LEU* 3.6 38.6 - - + -
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Residues in contact with SER 69 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45C LYS* 4.7 4.2 + - - +
65C ALA 2.8 19.7 + - - -
66C ALA* 2.7 24.7 + - - -
68C LEU* 1.3 72.4 - - - +
70C HIS* 1.3 69.0 + - - +
71C ILE 3.2 3.1 + - - +
77C VAL* 4.1 22.2 - - - +
179D THR* 3.4 18.5 - - - +
180D PHE* 5.4 0.2 - - - -
183D GLU* 4.7 3.9 - - - +
229D ARG* 5.8 0.9 + - - -
236D GLU* 5.4 0.3 + - - -
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Residues in contact with HIS 70 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66C ALA 3.5 7.0 + - - -
67C ASP 3.4 9.1 + - - +
68C LEU 3.1 1.6 - - - -
69C SER* 1.3 90.2 + - - +
71C ILE* 1.3 57.8 + - - +
172D LEU* 5.1 0.4 - - + -
175D VAL* 3.4 17.8 - - - +
176D ARG* 3.3 32.1 + - + +
179D THR* 2.8 22.9 + - - -
180D PHE* 3.7 19.8 - + - -
229D ARG* 5.0 1.3 - - - -
233D ALA* 3.6 25.6 - - + -
236D GLU* 3.1 23.8 + - - -
237D VAL* 3.4 27.8 - - + +
250D SER* 4.5 8.8 + - - -
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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