Contacts of the helix formed by residues 93 - 105 (chain B) in PDB entry 2ISZ
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 93 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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115A ARG* 5.1 5.2 - - - -
91B GLY 3.6 6.9 - - - +
92B LEU* 1.3 99.8 - - + +
94B TRP* 1.3 67.5 + - + +
95B GLU* 4.5 12.1 - - + -
96B GLU* 3.1 33.6 + - - +
97B VAL* 3.2 9.0 + - - +
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Residues in contact with TRP 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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84B ARG* 5.6 1.8 - - - -
87B VAL* 3.8 30.1 - - + -
92B LEU 3.4 3.8 + - - -
93B PRO* 1.3 71.8 - - + +
95B GLU* 1.3 78.3 + - - +
96B GLU 2.8 1.7 + - - -
97B VAL* 3.3 20.0 + - - +
98B HIS* 4.5 0.7 + - - +
127B PRO* 3.5 39.7 - - + -
128B PHE* 3.9 30.2 - + + -
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Residues in contact with GLU 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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93B PRO* 4.5 13.7 - - + -
94B TRP* 1.3 90.3 + - - +
96B GLU* 1.3 67.3 + - + +
98B HIS* 5.0 3.8 + - - +
99B ALA* 5.4 1.9 + - - +
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Residues in contact with GLU 96 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111A ASP* 3.5 34.8 - - - +
92B LEU* 3.9 14.5 - - + +
93B PRO* 3.1 27.7 + - + +
94B TRP 2.8 2.6 + - - -
95B GLU* 1.3 89.9 - - + +
97B VAL* 1.3 63.6 + - - +
98B HIS 3.2 2.7 - - - -
99B ALA* 3.1 13.6 + - + +
100B GLU* 3.1 19.8 + - - +
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Residues in contact with VAL 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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83B GLU* 4.1 7.6 - - + -
86B LEU* 3.7 16.6 - - + +
87B VAL* 3.9 23.6 - - + -
92B LEU* 3.4 37.7 - - + +
93B PRO 3.2 18.2 - - - +
94B TRP 3.3 3.7 + - - +
96B GLU* 1.3 76.4 - - - +
98B HIS* 1.3 60.3 + - - +
100B GLU* 3.6 1.3 - - - +
101B ALA* 2.8 32.3 + - - +
128B PHE* 3.3 31.6 - - + -
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Residues in contact with HIS 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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13B ARG* 4.4 16.1 + - - -
79B HIS* 3.2 11.9 + + - -
83B GLU* 3.6 12.3 - - - +
94B TRP 4.5 1.2 + - - +
95B GLU 5.0 3.3 + - - +
96B GLU 3.2 1.0 + - - -
97B VAL* 1.3 78.3 - - - +
99B ALA* 1.3 65.6 + - - +
101B ALA 3.3 0.9 + - - -
102B CYS* 2.9 37.7 + - + +
128B PHE* 4.5 9.8 - - + -
1001B NI 2.0 41.3 - - + +
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Residues in contact with ALA 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 GLU 5.4 1.7 + - - +
96B GLU* 3.1 15.5 + - + +
98B HIS* 1.3 85.3 - - - +
100B GLU* 1.3 64.1 + - - +
102B CYS* 3.3 14.8 + - - +
103B ARG* 3.7 20.5 + - - +
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Residues in contact with GLU 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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108A MET* 3.5 1.9 - - - -
109A SER* 2.7 42.9 + - - -
112A VAL* 3.5 13.5 - - + +
86B LEU* 3.8 22.2 - - + -
92B LEU* 3.9 8.5 - - + +
96B GLU 3.1 10.0 + - - +
97B VAL 3.6 7.0 - - - +
99B ALA* 1.3 79.9 - - - +
101B ALA* 1.3 57.5 + - - +
103B ARG* 2.8 41.7 + - - +
104B TRP* 2.9 45.1 + - + +
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Residues in contact with ALA 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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79B HIS* 3.4 35.2 + - - +
82B ALA* 3.8 16.2 - - + -
83B GLU* 3.5 15.3 - - + +
86B LEU* 4.0 4.4 - - + +
97B VAL 2.8 21.7 + - - +
98B HIS 3.9 1.8 - - - +
100B GLU* 1.3 72.5 - - - +
102B CYS* 1.3 56.2 + - - +
103B ARG 3.1 1.1 - - - -
104B TRP* 3.8 3.1 - - - +
105B GLU* 3.1 29.8 + - - +
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Residues in contact with CYS 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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4B LEU* 6.3 0.2 - - - -
5B VAL* 5.1 0.3 - - - +
10B MET* 3.8 13.0 - - - -
13B ARG* 4.2 7.4 - - - -
79B HIS* 3.9 6.1 - - + -
98B HIS* 2.9 25.8 + - + +
99B ALA* 3.4 11.0 - - - +
100B GLU 3.0 0.6 + - - -
101B ALA* 1.3 76.8 - - - +
103B ARG* 1.3 53.4 + - + +
105B GLU* 3.5 5.6 - - - -
106B HIS* 2.7 8.1 + - - -
1002B NI 2.0 75.7 - - - +
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Residues in contact with ARG 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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106A HIS 5.6 0.4 - - - -
107A VAL* 2.7 55.1 + - + +
109A SER* 3.6 16.0 - - - +
1B MET* 6.1 1.6 - - - -
3B GLU 5.3 4.9 - - - +
5B VAL* 4.1 18.1 - - + +
99B ALA* 3.7 22.8 + - - +
100B GLU* 2.8 37.5 + - - +
102B CYS* 1.3 80.1 - - + +
104B TRP* 1.3 66.7 + - + +
105B GLU 3.2 1.8 - - - -
106B HIS* 3.1 23.2 + - - +
107B VAL* 4.0 5.5 + - - +
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Residues in contact with TRP 104 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85A LEU* 4.6 3.6 - - + -
104A TRP* 3.6 39.3 - + + -
107A VAL* 3.9 21.7 + - + +
108A MET* 4.0 17.5 - - + +
112A VAL* 3.9 18.2 - - + -
116A LEU* 5.7 0.9 - - + -
82B ALA* 4.2 24.7 - - + -
85B LEU* 3.8 23.1 - - + -
86B LEU* 4.1 11.9 - - + -
90B ILE* 4.0 20.4 - - + -
100B GLU* 2.9 52.0 + - + +
101B ALA* 3.5 0.9 + - - +
103B ARG* 1.3 71.9 - - + +
105B GLU* 1.3 54.0 + - - +
106B HIS 2.8 15.3 + - - -
107B VAL* 2.9 20.5 + - + +
108B MET* 3.1 22.6 + - + +
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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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9B GLU* 4.1 4.7 - - - +
10B MET* 3.0 4.6 - - - +
13B ARG* 2.8 27.7 + - - -
75B VAL* 3.2 33.8 - - + +
78B LYS* 3.3 37.0 - - - +
79B HIS* 3.4 13.0 - - - +
82B ALA* 5.2 0.2 - - - +
101B ALA 3.1 19.4 + - - +
102B CYS 3.3 9.0 - - - +
104B TRP* 1.3 76.1 - - - +
106B HIS* 1.3 69.3 + - + +
107B VAL 3.4 0.2 - - - -
108B MET* 4.9 0.4 - - - -
1002B NI 1.9 41.9 - - - +
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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