Contacts of the helix formed by residues 82 - 92 (chain A) in PDB entry 4TQ1
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 PRO 82 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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41A ARG 4.0 0.9 - - - +
42A VAL 4.4 3.1 - - - +
43A SER 3.3 12.8 - - - +
44A TYR* 4.0 18.1 - - + +
80A HIS 3.8 7.0 - - - +
81A TYR* 1.3 85.4 - - + +
83A ILE* 1.3 67.7 + - - +
84A GLY 3.3 0.2 - - - -
85A LEU* 3.1 24.4 + - + +
86A LEU* 3.1 11.1 + - - +
260A TYR* 3.4 39.9 - - + -
262A ASP* 4.5 2.5 - - - +
266A HIS* 4.0 24.7 - - + +
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Residues in contact with ILE 83 (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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16A ILE* 4.2 13.5 - - + -
39A LEU* 4.1 20.0 - - + -
40A PRO 3.4 26.0 - - - +
41A ARG 3.6 0.4 + - - -
43A SER* 2.8 16.4 + - - +
44A TYR 3.6 19.7 - - - -
45A LEU* 3.6 29.2 - - + +
48A VAL* 3.6 22.7 - - + -
81A TYR 3.5 1.9 + - - -
82A PRO* 1.3 70.7 - - - +
84A GLY* 1.3 58.3 + - - +
86A LEU* 3.3 10.1 + - - +
87A PHE* 3.0 27.5 + - - +
98A TRP* 4.0 18.9 - - + -
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Residues in contact with GLY 84 (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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41A ARG* 2.7 51.2 + - - -
83A ILE* 1.3 74.1 - - - +
85A LEU* 1.3 56.4 + - - +
87A PHE* 3.9 3.0 - - - +
88A ASP* 3.0 36.4 + - - +
260A TYR* 3.5 8.7 - - - -
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Residues in contact with LEU 85 (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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81A TYR* 4.1 21.3 - - + -
82A PRO* 3.1 15.7 + - + +
84A GLY* 1.3 74.6 - - - +
86A LEU* 1.3 66.1 + - - +
88A ASP* 3.2 3.3 + - - +
89A LEU* 2.9 31.4 + - + +
190A TYR* 3.4 57.4 - - + +
260A TYR* 3.2 17.6 + - + +
266A HIS* 3.8 25.1 - - + +
268A SER* 3.4 23.3 - - - +
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Residues in contact with LEU 86 (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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45A LEU* 3.9 30.7 - - + -
77A LEU* 4.4 9.0 - - + -
78A LYS 3.6 26.5 - - - +
79A TRP* 5.0 0.4 - - - -
81A TYR* 3.7 29.6 - - + +
82A PRO 3.1 13.4 + - - +
83A ILE* 3.5 7.9 - - - +
85A LEU* 1.3 77.4 - - - +
87A PHE* 1.3 62.4 + - - +
89A LEU* 4.8 1.3 - - - -
90A LEU* 3.0 41.7 + - + +
98A TRP* 3.9 13.5 - - + -
194A THR* 3.9 24.9 - - + -
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Residues in contact with PHE 87 (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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16A ILE* 3.6 42.4 - - + -
41A ARG* 3.9 6.3 - - - -
83A ILE 3.0 15.9 + - - +
84A GLY 3.9 3.1 - - - +
86A LEU* 1.3 77.3 - - - +
88A ASP* 1.3 68.7 + - - +
91A ALA* 2.8 53.2 + - + +
92A SER* 3.0 28.3 + - - -
94A SER 4.8 3.6 - - - -
95A ALA 5.9 0.2 - - - -
96A LEU* 3.6 35.9 - - + -
98A TRP* 3.7 30.9 - + + -
593B GLU* 4.6 5.2 - - - -
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Residues in contact with ASP 88 (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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41A ARG* 3.0 28.8 + - - -
84A GLY 3.0 20.8 + - - +
85A LEU* 3.2 3.3 + - - +
87A PHE* 1.3 78.8 - - - +
89A LEU* 1.3 63.5 + - - +
92A SER* 2.6 27.7 + - - -
239A MET* 3.5 26.4 - - - +
240A ILE 4.1 0.2 - - - -
241A HIS 3.5 9.5 + - - -
242A GLY* 2.8 24.7 + - - -
260A TYR* 4.8 1.2 + - - -
268A SER* 3.7 15.7 - - - +
270A ILE* 3.4 10.2 - - - +
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Residues in contact with LEU 89 (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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85A LEU* 2.9 20.3 + - + +
86A LEU* 4.1 2.0 - - - +
88A ASP* 1.3 81.2 - - - +
90A LEU* 1.3 61.7 + - + +
190A TYR* 3.6 44.0 - - + +
192A THR* 3.8 32.9 - - - +
193A THR 3.8 18.2 - - - +
194A THR* 3.7 28.9 - - + -
268A SER* 3.8 16.4 - - - +
269A ILE 4.3 4.7 - - - +
270A ILE* 4.5 10.7 - - + +
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Residues in contact with LEU 90 (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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72A TYR* 3.5 29.3 + - + -
73A GLU* 5.0 1.4 - - - +
75A THR* 5.7 9.0 - - + -
77A LEU* 3.7 30.1 - - + -
86A LEU* 3.0 22.7 + - + +
89A LEU* 1.3 87.8 - - + +
91A ALA* 1.3 58.4 + - + +
92A SER 3.9 0.4 - - - -
93A SER* 5.6 1.2 + - - -
94A SER* 5.7 0.2 + - - -
98A TRP* 5.3 1.8 - - + +
192A THR 4.3 15.3 - - - +
193A THR* 4.4 3.6 - - + -
194A THR* 4.1 38.4 - - + +
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Residues in contact with ALA 91 (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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72A TYR* 3.4 22.0 - - + +
87A PHE* 2.8 26.7 + - + +
90A LEU* 1.3 75.0 - - + +
92A SER* 1.3 59.3 + - - +
93A SER* 3.1 6.1 - - - -
94A SER* 2.9 30.6 + - - +
98A TRP* 3.5 32.3 - - + +
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Residues in contact with SER 92 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A PHE* 3.0 24.9 + - - -
88A ASP* 2.6 33.6 + - - -
90A LEU 3.9 0.6 - - - -
91A ALA* 1.3 76.1 - - - +
93A SER* 1.3 60.5 + - - +
94A SER 3.3 4.6 + - - +
237A GLN* 5.1 0.9 + - - -
239A MET* 3.8 24.0 - - - +
270A ILE* 3.8 6.1 - - - +
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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