Contacts of the helix formed by residues 90 - 104 (chain B) in PDB entry 3NUI
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 SER 90 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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33A VAL 5.4 8.7 - - - -
80B PRO* 5.6 3.6 - - - -
88B ARG 3.4 3.6 + - - -
89B MET* 1.3 76.0 - - - +
91B ASP* 1.3 65.5 + - - +
92B GLN* 3.1 20.6 + - - -
93B THR* 2.7 31.8 + - - -
94B VAL* 3.2 19.6 + - - +
327B PRO* 3.4 18.7 - - - +
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Residues in contact with ASP 91 (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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32A VAL* 5.2 9.4 - - - +
34A THR* 5.6 5.0 - - - +
89B MET 3.8 1.9 + - - +
90B SER* 1.3 74.2 - - - +
92B GLN* 1.4 60.6 + - - +
94B VAL* 3.4 7.6 + - - +
95B MET* 3.0 44.6 + - + +
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Residues in contact with GLN 92 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75B GLN* 3.2 27.2 + - - +
80B PRO* 4.2 7.5 - - - +
90B SER* 3.1 22.2 + - - +
91B ASP* 1.4 78.8 + - + +
93B THR* 1.3 60.3 + - - +
95B MET* 3.3 8.9 + - - +
96B LEU* 2.8 30.7 + - - +
327B PRO* 3.6 25.9 + - - +
330B CYS* 3.7 2.6 - - + +
331B ALA* 3.9 24.9 - - + +
334B LEU* 3.9 7.1 - - + +
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Residues in contact with THR 93 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89B MET* 4.4 7.6 - - + -
90B SER* 2.7 27.5 + - - -
92B GLN* 1.3 74.4 - - - +
94B VAL* 1.3 66.2 + - - +
96B LEU* 3.2 2.3 + - - +
97B SER* 2.9 27.1 + - - +
113B TYR* 4.1 3.8 + - + -
323B ALA 3.5 13.9 - - - +
324B SER* 4.0 5.2 + - - -
325B GLY 3.3 43.3 + - - +
327B PRO* 4.0 4.3 - - - +
330B CYS* 3.8 16.5 - - - -
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Residues in contact with VAL 94 (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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89B MET* 4.3 31.0 - - + +
90B SER 3.2 14.5 + - - +
91B ASP* 3.7 10.1 - - - +
93B THR* 1.3 76.1 - - - +
95B MET* 1.3 60.0 + - + +
97B SER* 3.3 6.6 + - - -
98B GLU* 3.0 48.1 + - + +
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Residues in contact with MET 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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91B ASP* 3.0 30.6 + - - +
92B GLN* 3.6 7.2 - - - +
94B VAL* 1.3 77.9 - - + +
96B LEU* 1.3 65.4 + - - +
98B GLU* 3.5 16.2 + - - +
99B LYS* 3.1 22.2 + - - +
334B LEU* 3.7 20.8 - - + +
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Residues in contact with LEU 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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92B GLN 2.8 20.2 + - - +
93B THR 3.2 3.8 + - - +
95B MET* 1.3 72.2 - - - +
97B SER* 1.3 67.3 + - - +
99B LYS* 3.1 2.3 + - + -
100B LEU* 2.8 41.5 + - + +
113B TYR* 3.5 28.5 - - + +
287B LEU* 5.0 1.3 - - + -
294B MET* 4.0 5.2 - - + -
330B CYS* 3.8 24.5 - - + +
333B ALA* 3.8 26.9 - - + -
334B LEU* 3.9 17.6 - - + +
337B ILE* 3.8 22.2 - - + -
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Residues in contact with SER 97 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93B THR 2.9 12.7 + - - -
94B VAL* 3.3 11.0 + - - -
96B LEU* 1.3 74.5 - - - +
98B GLU* 1.3 62.4 + - - +
100B LEU* 3.4 1.6 + - - +
101B VAL* 3.1 28.9 + - - +
111B VAL* 3.8 20.0 + - - +
113B TYR* 2.8 31.5 + - - -
323B ALA* 4.5 3.8 + - - +
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Residues in contact with GLU 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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94B VAL* 3.0 37.0 + - + +
95B MET* 3.9 18.1 - - - +
96B LEU 3.1 0.4 - - - -
97B SER* 1.3 76.2 - - - +
99B LYS* 1.3 58.5 - - - +
101B VAL* 3.5 4.4 + - - +
102B GLU* 2.8 31.1 + - - +
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Residues in contact with LYS 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 MET 3.1 13.8 + - - +
96B LEU* 3.1 8.6 + - + +
98B GLU* 1.3 77.3 - - - +
100B LEU* 1.3 56.9 + - - +
102B GLU* 3.2 28.0 + - - +
103B VAL* 2.8 45.5 + - + +
334B LEU* 3.7 22.7 - - + +
337B ILE* 4.2 29.6 - - + -
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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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96B LEU* 2.8 40.9 + - + +
97B SER 3.8 4.0 - - - +
99B LYS* 1.3 74.0 - - - +
101B VAL* 1.3 59.6 + - - +
103B VAL* 3.3 5.0 + - + +
104B SER* 2.8 33.5 + - - -
111B VAL* 4.1 19.3 - - + -
113B TYR* 3.7 11.9 - - - +
262B PHE* 3.9 13.5 - - + -
269B TRP* 5.3 0.2 - - + -
283B SER* 5.5 0.7 - - - +
287B LEU* 3.8 24.5 - - + -
296B ALA* 4.2 15.7 - - + -
298B ILE* 4.1 22.9 - - + +
337B ILE* 3.8 16.6 - - + -
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Residues in contact with VAL 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 SER* 3.1 17.3 + - - +
98B GLU* 3.9 4.7 - - - +
100B LEU* 1.3 74.5 - - - +
102B GLU* 1.3 65.3 + - - +
104B SER* 2.8 24.4 + - - +
106B PHE* 3.3 12.6 - - + +
107B ASP 4.3 4.7 - - - +
108B SER* 3.6 33.2 - - - +
109B GLY* 3.7 26.7 - - - +
110B ARG 4.4 0.2 - - - +
111B VAL* 3.9 17.0 - - + -
298B ILE* 4.5 7.2 - - + -
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Residues in contact with GLU 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 GLU 2.8 18.2 + - - +
99B LYS* 3.4 36.0 + - - +
101B VAL* 1.3 80.4 - - - +
103B VAL* 1.3 67.8 + - + +
104B SER 3.4 5.9 + - - +
106B PHE 4.9 1.9 - - - +
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Residues in contact with VAL 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 LYS* 2.8 46.0 + - + +
100B LEU* 3.8 11.2 - - + +
102B GLU* 1.3 78.0 - - - +
104B SER* 1.3 68.1 + - - +
262B PHE* 3.9 28.0 - - + -
268B THR* 4.4 4.8 - - + +
269B TRP* 2.9 22.9 + - + -
337B ILE* 4.9 0.9 - - + -
341B MET* 3.9 31.9 - - + -
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Residues in contact with SER 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 LEU 2.8 16.0 + - - -
101B VAL* 2.8 18.6 + - - +
102B GLU 3.4 8.5 - - - +
103B VAL* 1.3 82.3 - - - +
105B PRO* 1.4 71.9 - - - +
106B PHE* 3.0 37.6 + - - +
269B TRP* 3.5 11.7 - - - +
281B ILE* 4.5 4.3 - - - -
298B ILE* 4.2 9.9 - - - -
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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