Contacts of the helix formed by residues 94 - 107 (chain B) in PDB entry 5U8T
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 THR 94 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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90B PRO 4.8 0.5 + - - -
91B GLN* 4.5 7.8 + - - -
92B TRP 3.3 3.4 + - - -
93B LEU* 1.3 81.2 + - - +
95B THR* 1.3 75.6 + - + +
96B LYS* 3.6 36.3 - - + +
97B GLU* 3.4 9.8 + - - -
98B LEU* 3.0 28.6 + - - +
135B HIS* 5.0 15.6 - - + -
141B LEU* 4.3 9.4 - - - +
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Residues in contact with THR 95 (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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94B THR* 1.3 78.0 - - + +
96B LYS* 1.3 72.8 + - + +
98B LEU* 3.0 23.7 + - - +
99B ASP* 3.0 22.6 + - - +
135B HIS 6.0 2.0 - - - +
136B ASP* 5.8 2.2 - - + +
140B GLU* 4.1 29.7 + - + -
141B LEU* 4.3 9.9 - - + +
144B LYS* 5.2 6.1 - - - +
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Residues in contact with LYS 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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94B THR* 3.6 19.7 - - + -
95B THR* 1.3 83.1 - - + +
97B GLU* 1.3 64.8 + - - +
99B ASP* 3.6 22.0 - - - +
100B ARG* 3.6 17.6 + - - +
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Residues in contact with GLU 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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91B GLN 4.7 4.0 - - - +
92B TRP* 2.8 41.4 - - - +
94B THR* 3.4 16.8 + - - +
95B THR 3.0 0.2 - - - -
96B LYS* 1.3 84.5 - - + +
98B LEU* 1.3 79.7 + - - +
99B ASP 3.0 1.3 - - - -
100B ARG* 2.9 34.7 + - - +
101B LYS* 2.4 45.5 + - - +
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Residues in contact with LEU 98 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92B TRP* 4.6 20.9 - - + +
94B THR 3.0 20.7 + - - +
95B THR* 3.0 6.8 + - - +
97B GLU* 1.3 86.8 + - - +
99B ASP* 1.3 58.8 + - - +
101B LYS* 3.3 5.1 + - + +
102B ILE* 2.9 40.8 + - + +
119B TRP* 6.5 0.4 - - + -
141B LEU* 3.5 32.1 - - + -
144B LYS* 3.5 35.2 - - + -
145B ILE* 4.1 11.7 - - + -
148B LEU* 4.1 18.6 - - + -
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Residues in contact with ASP 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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95B THR* 3.0 23.8 + - - +
96B LYS* 3.6 16.7 - - - +
97B GLU 3.0 0.6 - - - -
98B LEU* 1.3 78.1 - - - +
100B ARG* 1.3 62.8 + - - +
102B ILE* 3.2 18.7 - - - +
103B GLN* 2.9 35.7 + - + +
144B LYS* 5.0 13.2 + - - +
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Residues in contact with ARG 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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96B LYS* 3.6 18.3 + - - +
97B GLU* 2.9 30.6 + - - +
99B ASP* 1.3 74.8 - - - +
101B LYS* 1.3 84.9 + - + +
103B GLN* 3.8 9.0 - - - +
104B TYR* 3.0 28.1 + - - +
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Residues in contact with LYS 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 GLU* 2.4 46.6 + - - +
98B LEU* 3.8 7.4 - - + +
100B ARG* 1.3 103.4 - - + +
102B ILE* 1.3 58.7 + - + +
104B TYR* 3.2 9.8 + - + +
105B GLU* 2.9 25.1 + - - +
113B SER* 4.2 12.2 + - - +
114B GLU* 4.0 35.2 - - + +
115B LEU* 5.4 4.7 - - + -
148B LEU* 5.2 7.9 - - + -
152B ARG* 5.8 1.6 - - - +
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Residues in contact with ILE 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 LEU* 2.9 32.3 + - + +
99B ASP* 3.2 26.2 - - - +
101B LYS* 1.3 69.4 - - - +
103B GLN* 1.3 67.0 + - + +
105B GLU* 3.1 10.9 + - - +
106B LYS* 2.9 39.9 + - - +
144B LYS* 4.5 16.2 - - + +
147B ASP* 5.8 5.2 - - + +
148B LEU* 3.6 41.1 - - + -
151B ILE* 4.0 9.2 - - + +
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Residues in contact with GLN 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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99B ASP* 2.9 25.1 + - + +
100B ARG* 3.8 8.1 - - - +
102B ILE* 1.3 79.4 - - + +
104B TYR* 1.3 64.6 + - - +
105B GLU 3.0 1.3 - - - -
106B LYS* 3.1 13.6 + - + +
107B THR* 3.0 26.5 + - - +
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Residues in contact with TYR 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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100B ARG 3.0 16.1 + - - +
101B LYS* 3.2 14.6 + - + +
103B GLN* 1.3 74.8 - - - +
105B GLU* 1.3 61.8 + - - +
107B THR* 3.6 7.4 - - - -
108B HIS* 2.5 67.0 + + + +
111B ARG* 2.6 36.9 + - + -
113B SER* 3.3 35.9 - - - -
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Residues in contact with GLU 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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1045 LEU* 5.3 0.7 - - - +
101B LYS 2.9 11.3 + - - +
102B ILE* 3.1 15.9 - - - +
103B GLN 3.0 0.4 - - - -
104B TYR* 1.3 79.0 - - - +
106B LYS* 1.3 59.8 + - - +
108B HIS* 3.3 5.1 - - - +
109B PRO* 4.6 0.5 - - - +
112B PHE* 2.9 33.9 - - - +
113B SER* 3.0 10.2 + - - -
148B LEU* 5.4 1.1 - - + +
151B ILE* 3.6 29.6 - - + -
152B ARG* 3.4 25.0 + - - +
155B LYS* 2.7 57.1 + - - +
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Residues in contact with LYS 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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1005 ARG* 5.5 8.9 - - - +
1045 LEU* 3.2 53.3 - - + +
1065 ARG 5.0 4.7 - - - -
102B ILE* 2.9 26.9 + - - +
103B GLN* 3.1 13.9 + - + +
105B GLU* 1.3 75.8 - - - +
107B THR* 1.3 59.7 + - - +
108B HIS 3.5 0.7 + - - -
109B PRO* 4.3 7.1 - - - +
147B ASP* 5.3 9.0 + - - -
151B ILE* 4.6 20.6 - - + -
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Residues in contact with THR 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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1065 ARG 5.9 2.5 - - - -
103B GLN 3.0 20.2 + - - +
104B TYR* 3.3 5.2 - - + +
106B LYS* 1.3 75.7 - - - +
108B HIS* 1.3 88.6 + - + +
109B PRO* 3.6 8.3 - - - +
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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