Contacts of the helix formed by residues 92 - 104 (chain B) in PDB entry 1NUS
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 GLU 92 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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90B TRP* 3.8 27.4 - - + +
91B MET* 1.3 79.4 - - - +
93B THR* 1.3 67.3 + - - +
94B VAL* 4.2 7.0 - - + -
95B LYS* 3.0 52.1 + - + +
96B VAL* 3.4 4.2 + - - +
149B LYS* 5.1 3.5 - - + +
152B HIS* 3.7 28.1 - - + +
302B SO4 4.2 2.3 + - - -
402B NMN 3.6 15.7 - - - +
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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
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12B CYS* 4.1 15.2 - - + +
84B GLU* 5.6 1.4 + - - -
91B MET 3.5 1.8 + - - -
92B GLU* 1.3 69.3 - - - +
94B VAL* 1.3 65.9 - - - +
96B VAL* 2.9 20.3 + - - +
97B LEU* 2.9 14.9 + - + +
132B LEU* 3.9 39.0 - - + -
148B TRP* 4.1 18.8 - - + -
156B ILE* 4.9 1.1 - - + -
402B NMN 3.2 39.1 + - - -
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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
----------------------------------------------------------
92B GLU* 4.2 3.1 - - + +
93B THR* 1.3 76.6 - - - +
95B LYS* 1.3 70.7 + - + +
97B LEU* 3.0 13.3 + - - +
98B ARG* 2.9 47.3 + - - +
152B HIS* 3.4 59.2 - - + +
155B GLU* 4.6 10.1 - - + +
156B ILE* 3.4 30.5 - - + -
160B PHE* 4.5 1.4 - - + -
402B NMN 4.8 1.3 + - - +
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Residues in contact with LYS 95 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83B TRP* 4.7 0.3 - - - -
91B MET* 3.4 25.3 - - + +
92B GLU* 3.0 48.3 + - + +
94B VAL* 1.3 83.3 - - + +
96B VAL* 1.3 59.5 + - - +
98B ARG* 3.4 23.0 + - - +
99B HIS* 3.2 22.2 + - - +
302B SO4 3.5 32.2 + - - -
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Residues in contact with VAL 96 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10B LEU* 4.0 12.1 - - + -
12B CYS* 4.1 7.9 - - - -
47B SER* 4.1 4.5 - - - +
83B TRP* 4.4 9.2 - - + -
84B GLU* 3.5 46.0 - - + +
91B MET* 4.3 13.9 - - - +
92B GLU 3.4 11.0 + - - +
93B THR* 2.9 12.7 + - - +
95B LYS* 1.3 78.5 - - - +
97B LEU* 1.3 62.6 + - - +
99B HIS* 3.5 0.9 + - - +
100B HIS* 3.2 44.5 + - + +
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Residues in contact with LEU 97 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10B LEU* 3.6 25.8 - - + -
93B THR* 2.9 22.0 + - + +
94B VAL* 3.0 8.7 + - - +
96B VAL* 1.3 75.8 - - - +
98B ARG* 1.3 60.0 + - - +
101B HIS* 3.0 24.9 + - - +
130B LEU* 3.1 31.7 - - + +
132B LEU* 4.3 35.0 - - + +
156B ILE* 4.1 24.2 - - + -
160B PHE* 3.5 33.5 - - + -
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Residues in contact with ARG 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* 2.9 32.8 + - - +
95B LYS* 3.8 22.7 - - - +
97B LEU* 1.3 74.4 - - - +
99B HIS* 1.3 66.2 + - - +
101B HIS* 2.9 8.2 + - - +
102B SER* 2.9 26.3 + - - +
152B HIS* 4.7 0.8 + - - -
155B GLU* 2.7 43.1 + - - +
159B LYS* 5.1 4.3 - - - -
160B PHE* 3.9 11.4 - - + -
302B SO4 2.9 40.8 + - - -
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Residues in contact with HIS 99 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83B TRP* 3.0 82.0 - + + +
95B LYS 3.2 8.8 + - - +
96B VAL 3.8 1.8 - - - +
97B LEU 3.4 0.2 - - - -
98B ARG* 1.3 78.7 - - - +
100B HIS* 1.3 76.6 + + - +
102B SER* 3.1 12.8 + - - -
103B LYS* 3.0 50.9 + - + +
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Residues in contact with HIS 100 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10B LEU* 4.3 16.0 - - + +
45B ILE* 4.2 18.0 - - + +
47B SER* 4.6 5.3 + - - -
79B ARG* 4.8 0.4 + - - -
81B ASP* 3.1 45.6 + - + +
83B TRP* 4.5 5.1 - - - +
84B GLU 5.3 0.2 + - - -
96B VAL* 3.2 42.9 + - + +
99B HIS* 1.3 95.2 - + - +
101B HIS* 1.3 64.5 + - - +
103B LYS* 3.7 13.3 - - + +
104B LEU* 3.2 27.4 + - - +
130B LEU* 3.9 20.2 - - + -
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Residues in contact with HIS 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 LEU 3.0 19.2 + - - +
98B ARG* 2.9 7.8 + - - +
100B HIS* 1.3 76.2 - - - +
102B SER* 1.3 66.2 + - - +
104B LEU* 3.3 25.5 + - - +
105B LEU* 3.4 32.1 - - + +
127B VAL* 5.3 3.1 - - + -
128B PRO 5.2 6.7 + - - -
130B LEU* 3.6 11.5 + - + +
159B LYS* 3.5 31.4 + - - -
160B PHE* 3.7 16.7 - + + -
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Residues in contact with SER 102 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98B ARG* 2.9 16.2 + - - +
99B HIS* 3.1 13.7 - - - -
101B HIS* 1.3 76.5 - - - +
103B LYS* 1.3 65.4 + - - +
105B LEU* 2.9 29.6 + - - +
106B ARG 3.5 7.2 + - - +
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Residues in contact with LYS 103 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79B ARG* 4.0 12.2 - - - +
81B ASP* 3.2 21.0 + - - +
83B TRP* 6.1 0.2 - - - +
99B HIS* 3.0 46.0 + - + +
100B HIS* 3.7 20.6 - - - +
101B HIS 3.4 0.4 - - - -
102B SER* 1.3 75.1 - - - +
104B LEU* 1.3 55.2 + - + +
106B ARG* 2.7 34.2 + - - +
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Residues in contact with LEU 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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8B VAL* 3.8 30.7 - - + -
42B ILE* 5.9 0.4 - - + -
45B ILE* 6.3 1.6 - - + -
100B HIS 3.2 15.6 + - - +
101B HIS* 3.3 15.7 - - - +
102B SER 3.1 0.4 - - - -
103B LYS* 1.3 78.5 - - + +
105B LEU* 1.3 56.0 + - - +
106B ARG* 2.6 37.2 + - - +
127B VAL* 4.3 15.8 - - + +
128B PRO* 4.0 26.3 - - + +
130B LEU* 3.9 31.2 - - + -
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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