Contacts of the helix formed by residues 95 - 108 (chain B) in PDB entry 5DQZ
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 ARG 95 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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203A ALA* 4.4 2.9 - - - -
210A GLY 6.0 1.3 - - - -
93B GLY 3.4 0.2 - - - -
94B ALA* 1.3 83.1 - - + +
96B SER* 1.3 65.6 + - - +
97B ASP* 2.9 35.7 + - - +
98B LYS* 3.5 36.0 + - + +
99B LEU* 3.5 16.6 + - - +
199B GLY* 4.6 1.6 + - - +
293B LEU* 6.1 3.4 - - + -
300B ALA* 3.4 39.8 - - - +
301B GLY* 5.3 1.1 - - - -
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Residues in contact with SER 96 (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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203A ALA* 2.7 34.6 + - - +
204A ILE* 4.6 7.4 - - - -
205A GLY 5.4 0.4 - - - -
209A THR* 5.1 5.8 - - - -
210A GLY* 3.2 30.9 + - - -
211A LYS 3.6 5.7 + - - -
94B ALA 4.1 1.4 + - - -
95B ARG* 1.3 71.4 - - - +
97B ASP* 1.3 59.8 + - - +
99B LEU* 3.2 4.9 + - - +
100B LEU* 2.9 40.7 + - - +
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Residues in contact with ASP 97 (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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210A GLY* 6.0 0.2 - - - -
95B ARG* 2.9 48.8 + - - +
96B SER* 1.3 75.7 + - - +
98B LYS* 1.3 64.9 + - - +
100B LEU* 3.9 7.8 - - - -
101B TYR* 2.9 30.3 + - - +
279B PRO* 4.0 15.7 - - + +
280B PRO* 3.7 26.6 - - - +
282B PRO* 6.1 2.2 - - + -
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Residues in contact with LYS 98 (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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95B ARG* 3.7 41.7 - - + +
96B SER 3.2 0.6 - - - -
97B ASP* 1.3 87.0 + - - +
99B LEU* 1.3 58.0 + - - +
101B TYR* 3.1 10.1 - - + +
102B GLN 2.9 24.4 + - - -
198B ALA* 3.0 23.5 + - - +
199B GLY* 3.6 17.9 - - - +
200B TYR* 3.4 28.3 + - + +
265B ILE* 6.0 0.2 - - - +
269B GLU* 2.7 30.5 + - - -
279B PRO* 5.4 6.5 - - + -
300B ALA* 4.3 13.0 - - + +
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Residues in contact with LEU 99 (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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201A ALA* 4.4 13.5 - - + -
203A ALA* 4.0 21.8 - - + -
204A ILE* 3.8 22.8 - - + +
93B GLY* 4.3 19.5 - - - +
95B ARG 3.5 13.4 + - - +
96B SER 3.2 6.1 + - - +
98B LYS* 1.3 75.2 - - - +
100B LEU* 1.3 58.2 + - - +
102B GLN* 3.4 9.1 + - - +
103B ALA* 2.9 30.1 + - - +
199B GLY 3.3 20.6 - - - +
200B TYR* 3.8 2.7 - - - -
201B ALA* 3.8 30.3 - - + +
204B ILE* 5.4 2.1 - - + +
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Residues in contact with LEU 100 (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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103A ALA* 4.3 7.6 - - + +
106A ALA* 3.9 18.8 - - + +
107A LEU* 4.1 22.2 - - + +
204A ILE* 3.7 37.9 - - + -
205A GLY 5.9 2.0 - - - +
209A THR* 6.2 4.0 - - + -
96B SER* 2.9 30.0 + - - +
97B ASP* 4.0 3.8 - - - +
99B LEU* 1.3 73.5 - - - +
101B TYR* 1.3 59.8 + - - +
103B ALA* 3.9 2.7 - - - +
104B LYS* 2.9 31.7 + - - +
280B PRO* 3.9 21.8 - - + +
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Residues in contact with TYR 101 (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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97B ASP 2.9 20.4 + - - +
98B LYS* 3.1 5.4 - - + +
100B LEU* 1.3 74.7 - - - +
102B GLN* 1.3 66.7 + - - +
104B LYS* 3.7 3.6 - - - +
105B LEU* 2.9 43.8 + - + +
200B TYR* 3.7 26.0 - + - -
269B GLU* 4.5 6.0 + - - -
272B LEU* 3.2 44.3 + - + +
273B ALA* 3.3 11.8 + - - +
277B ILE* 3.1 30.8 + - + -
278B GLN 4.1 2.9 - - - -
279B PRO* 3.6 37.5 - - + -
280B PRO* 3.9 7.6 - - + +
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Residues in contact with GLN 102 (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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98B LYS 2.9 11.9 + - - +
99B LEU* 3.7 10.8 - - - +
100B LEU 3.4 0.2 - - - -
101B TYR* 1.3 77.8 - - - +
103B ALA* 1.3 57.3 + - - +
105B LEU* 3.3 12.9 + - - +
106B ALA* 2.9 27.0 + - - +
200B TYR* 3.5 18.1 - - + +
201B ALA* 2.8 50.7 + - - +
204B ILE* 3.0 34.1 + - + +
206B PHE* 4.0 10.5 - - + -
215B PHE* 3.4 18.8 - - - -
272B LEU* 4.9 5.4 - - + -
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Residues in contact with ALA 103 (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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100A LEU* 4.3 13.5 - - + -
103A ALA* 3.5 31.0 - - + -
107A LEU* 4.4 2.7 - - + -
99B LEU 2.9 18.8 + - - +
100B LEU* 3.9 4.5 - - - +
102B GLN* 1.3 74.8 - - - +
104B LYS* 1.3 61.0 + - - +
106B ALA* 3.2 6.6 + - - +
107B LEU* 2.9 36.9 + - + +
204B ILE* 4.6 9.2 - - + -
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Residues in contact with LYS 104 (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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107A LEU* 3.6 31.6 - - + +
100B LEU 2.9 19.0 + - - +
101B TYR* 3.7 4.7 - - - +
103B ALA* 1.3 75.3 - - - +
105B LEU* 1.3 62.7 + - + +
107B LEU* 4.2 2.5 - - - +
108B ASP* 3.4 25.3 + - + +
111B LEU* 3.9 14.7 - - + +
277B ILE* 4.9 26.1 - - + +
278B GLN 5.6 1.6 + - - -
280B PRO* 5.1 16.1 - - + +
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Residues in contact with LEU 105 (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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101B TYR* 2.9 40.0 + - + +
102B GLN 3.5 7.2 - - - +
104B LYS* 1.3 76.9 - - - +
106B ALA* 1.3 59.9 + - - +
108B ASP 3.4 4.9 - - - +
111B LEU* 3.8 21.5 - - + +
112B ARG* 3.2 27.5 + - - -
115B VAL* 4.2 6.1 - - + -
206B PHE* 3.6 12.1 - - + -
272B LEU* 3.5 47.3 - - + +
275B GLY* 3.9 28.3 - - - -
277B ILE* 5.0 7.9 - - + -
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Residues in contact with ALA 106 (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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100A LEU* 4.8 6.1 - - + -
102B GLN 2.9 17.2 + - - +
103B ALA* 3.2 4.7 + - - +
105B LEU* 1.3 77.1 - - - +
107B LEU* 1.3 61.7 + - - +
109B GLU* 5.5 1.0 - - - +
112B ARG* 3.9 19.1 - - - -
204B ILE* 3.6 26.7 - - + -
205B GLY 4.4 6.7 - - - +
206B PHE* 3.5 19.5 - - + -
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Residues in contact with LEU 107 (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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100A LEU* 3.9 39.0 - - + +
104A LYS* 4.1 39.9 - - + +
107A LEU* 4.6 9.2 - - + -
103B ALA* 2.9 24.4 + - + +
104B LYS* 3.6 4.0 + - - +
105B LEU 3.4 0.2 - - - -
106B ALA* 1.3 78.7 - - - +
108B ASP* 1.3 63.2 + - - +
109B GLU* 3.5 11.1 + - - +
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Residues in contact with ASP 108 (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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104B LYS* 3.4 15.7 + - + +
105B LEU 3.4 1.0 - - - +
106B ALA 4.6 0.2 - - - -
107B LEU* 1.3 78.2 - - - +
109B GLU* 1.3 62.8 + - - +
110B ASP* 3.1 25.4 + - - +
111B LEU* 3.8 24.1 - - + +
112B ARG* 2.8 30.9 + - - +
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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