Contacts of the helix formed by residues 60 - 70 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241A LYS* 5.0 3.8 + - - +
244A ALA* 4.0 28.4 - - + +
33B SER* 3.5 17.5 - - - +
38B GLN* 5.7 1.6 - - - +
59B ALA* 1.3 90.0 - - + +
61B THR* 1.3 62.6 + - - +
62B PRO* 3.3 7.3 - - - +
63B GLY* 3.1 14.0 + - - -
64B VAL* 3.1 16.4 + - + +
81B LEU* 4.0 5.3 - - - +
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Residues in contact with THR 61 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32B ALA* 4.2 4.5 - - + -
33B SER* 3.6 5.8 - - - +
55B LEU* 3.5 34.0 - - + +
56B TYR 3.7 4.3 - - - +
57B ASP* 3.5 26.9 + - + +
59B ALA 3.1 3.2 + - - -
60B HIS* 1.3 73.1 - - - +
62B PRO* 1.4 60.1 - - - +
64B VAL* 3.2 4.5 + - + +
65B ALA* 2.8 32.8 + - - +
79B GLY* 4.5 1.1 - - - -
80B TYR 2.8 24.0 + - - -
81B LEU* 3.4 17.5 - - - +
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Residues in contact with PRO 62 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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240A ALA* 4.1 12.4 - - + +
60B HIS* 3.3 6.7 - - - -
61B THR* 1.4 96.8 - - - +
63B GLY* 1.3 54.8 + - - +
65B ALA* 4.0 4.5 - - + +
66B ALA* 3.0 29.1 + - - +
79B GLY* 4.9 8.3 - - - +
80B TYR 5.5 0.2 - - - -
81B LEU* 4.1 29.2 - - + -
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Residues in contact with GLY 63 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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237A VAL* 4.4 1.0 - - - +
240A ALA* 3.6 25.5 + - - -
241A LYS* 3.7 26.6 - - - +
60B HIS 3.1 7.5 + - - -
62B PRO* 1.3 76.2 - - - +
64B VAL* 1.3 65.2 + - - +
66B ALA* 3.7 1.6 - - - +
67B ASP* 3.1 24.4 + - - +
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Residues in contact with VAL 64 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241A LYS* 4.8 7.2 - - - +
249A LEU* 4.0 21.8 - - + -
32B ALA* 4.3 8.1 - - + +
33B SER* 3.9 14.6 - - - +
38B GLN* 3.8 36.8 - - + +
41B SER* 5.4 0.7 - - - -
55B LEU* 4.1 9.4 - - + -
60B HIS* 3.1 17.7 + - + +
61B THR* 3.8 8.5 - - + +
63B GLY* 1.3 76.5 - - - +
65B ALA* 1.3 57.6 + - - +
67B ASP* 3.4 6.9 - - - +
68B LEU* 3.0 37.4 + - + +
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Residues in contact with ALA 65 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55B LEU* 4.0 14.8 - - + +
61B THR 2.8 17.5 + - - +
62B PRO* 4.0 3.1 - - + +
64B VAL* 1.3 75.4 - - - +
66B ALA* 1.3 59.1 + - - +
68B LEU 3.4 0.3 + - - -
69B SER* 2.8 33.6 + - - -
77B VAL* 3.9 7.8 - - + +
78B LYS* 3.9 5.6 - - - -
79B GLY* 3.4 31.9 - - - +
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Residues in contact with ALA 66 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236A GLU 5.2 1.6 - - - +
237A VAL* 4.3 12.8 - - + -
240A ALA* 3.9 19.5 - - + -
62B PRO 3.0 19.6 + - - +
63B GLY 3.7 5.2 - - - +
64B VAL 3.5 0.2 - - - -
65B ALA* 1.3 75.3 - - - +
67B ASP* 1.3 64.3 + - - +
69B SER* 2.6 23.8 + - - -
70B HIS* 3.4 14.3 + - - +
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Residues in contact with ASP 67 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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237A VAL* 4.2 18.3 - - + +
241A LYS* 3.4 7.3 + - - -
247A ALA* 3.9 4.3 - - - -
248A THR* 2.8 33.3 + - - -
249A LEU* 3.0 18.4 + - + +
250A SER* 2.6 57.7 + - - -
38B GLN* 5.4 0.2 - - - +
63B GLY 3.1 16.4 + - - +
64B VAL* 3.4 8.0 - - - +
66B ALA* 1.3 81.1 - - - +
68B LEU* 1.3 62.6 + - - +
69B SER 3.3 0.2 + - - -
70B HIS* 3.3 7.3 + - - +
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Residues in contact with LEU 68 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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249A LEU* 3.6 33.2 - - + -
41B SER* 3.6 32.1 - - - +
42B LEU* 3.6 26.5 - - - -
45B LYS* 3.3 22.0 - - + -
53B LEU* 4.8 2.7 - - + -
55B LEU* 3.8 19.1 - - + -
64B VAL* 3.0 17.1 + - + +
65B ALA 4.0 2.5 - - - +
67B ASP* 1.3 76.5 - - - +
69B SER* 1.3 61.7 + - - +
70B HIS 3.1 1.4 + - - -
71B ILE* 3.1 31.0 + - + +
77B VAL* 4.2 12.3 - - + -
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Residues in contact with SER 69 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179A THR* 3.4 17.8 - - - +
180A PHE* 5.2 0.7 - - - -
183A GLU* 4.3 8.7 - - - +
229A ARG* 5.3 3.3 + - - -
45B LYS* 4.7 3.3 + - - +
65B ALA 2.8 19.5 + - - -
66B ALA* 2.6 23.7 + - - -
68B LEU* 1.3 72.1 - - - +
70B HIS* 1.3 67.6 + - - +
71B ILE 3.3 2.8 + - - +
77B VAL* 4.2 25.5 - - - +
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Residues in contact with HIS 70 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172A LEU* 4.9 0.7 - - + -
175A VAL* 3.3 18.9 - - - +
176A ARG* 3.2 33.1 + - + +
179A THR* 2.9 19.7 + - - -
180A PHE* 3.6 22.8 - + - -
229A ARG* 4.3 9.7 + - - -
233A ALA* 3.6 27.6 - - + -
236A GLU* 5.5 4.0 - - + +
237A VAL* 3.5 28.4 - - + +
250A SER* 4.4 8.0 + - - -
66B ALA* 3.4 16.0 + - - +
67B ASP 3.3 9.6 + - - +
68B LEU 3.1 1.2 - - - -
69B SER* 1.3 83.9 + - - +
71B ILE* 1.3 59.2 + - - +
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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