Contacts of the strand formed by residues 83 - 93 (chain B) in PDB entry 2IZM
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 83 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55A ASN* 5.5 0.7 + - - -
91A THR* 4.3 0.3 - - - +
93A PRO* 3.3 17.2 - - - +
38B ARG 4.2 7.9 + - - -
39B SER* 2.9 35.4 + - - +
40B GLN* 3.8 5.7 - - - +
41B ALA 2.6 28.9 + - - -
43B LYS* 4.9 1.8 - - - +
63B GLU* 3.0 43.1 + - - +
64B VAL 3.5 5.4 - - - +
65B PRO* 3.8 15.5 - - - +
66B LYS 4.7 0.9 - - - +
79B VAL* 3.5 24.4 + - - +
80B ALA 3.7 5.9 - - - +
81B ALA 3.6 1.0 - - - -
82B TRP* 1.3 87.3 + - + +
84B SER* 1.3 63.8 + - - +
85B TYR* 3.7 36.6 + - + +
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Residues in contact with SER 84 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90A LEU* 4.9 4.0 - - - -
91A THR 3.2 9.4 - - - -
92A ILE* 3.6 6.0 - - - +
93A PRO* 3.3 19.8 - - - +
96A ALA* 5.2 1.6 - - - +
104A ILE* 3.4 34.4 - - - +
62B VAL 3.8 0.3 - - - +
63B GLU* 3.4 6.6 - - - +
64B VAL* 2.8 39.4 + - - +
83B ARG* 1.3 73.6 - - - +
85B TYR* 1.3 64.1 + - - +
86B LEU 4.3 0.2 - - - -
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Residues in contact with TYR 85 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89A GLU 3.4 2.1 - - - +
90A LEU* 3.3 6.5 - - - +
91A THR* 2.8 53.5 + - + +
62B VAL 3.6 2.0 - - - -
63B GLU* 3.6 37.6 + - + -
79B VAL* 4.0 13.3 + - - +
80B ALA* 5.2 9.8 - - + -
83B ARG* 3.7 44.7 - - + +
84B SER* 1.3 72.6 - - - +
86B LEU* 1.3 61.8 + - - +
87B ASN* 5.6 0.9 - - + -
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Residues in contact with LEU 86 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A MET* 4.3 23.6 - - + -
89A GLU 3.5 6.7 - - - +
90A LEU* 4.0 20.6 - - + -
104A ILE* 5.9 1.6 - - + -
108A MET* 3.5 43.3 - - + -
111A LEU* 5.1 2.0 - - + -
60B ILE 5.4 0.4 - - - +
61B LYS* 3.4 7.6 - - - +
62B VAL* 2.8 65.3 + - + +
64B VAL* 6.2 1.3 - - + -
85B TYR* 1.3 73.3 - - - +
87B ASN* 1.3 63.5 + - - +
88B MET* 4.4 21.8 - - + +
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Residues in contact with ASN 87 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A ASN 3.4 2.3 - - - +
88A MET* 3.0 4.9 - - - -
89A GLU* 2.9 50.1 + - + +
59B THR* 4.8 2.4 - - - +
60B ILE 3.9 1.6 - - - -
61B LYS* 2.9 37.7 + - - +
85B TYR* 5.6 1.1 - - + -
86B LEU* 1.3 75.4 + - - +
88B MET* 1.3 63.1 + - - +
89B GLU* 4.1 19.6 - - - +
5R G 5.2 3.8 + - - -
6R C 4.2 7.1 + - - -
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Residues in contact with MET 88 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A LEU* 3.7 22.2 - - + -
87A ASN 3.5 2.9 - - - +
88A MET* 3.5 35.7 - - + -
108A MET* 6.4 0.4 - - - +
111A LEU* 4.2 22.0 - - - -
112A LEU* 4.6 11.7 - - + -
58B TYR 3.8 0.3 - - - +
59B THR* 3.5 3.1 - - - +
60B ILE* 2.8 64.8 + - + +
86B LEU* 4.4 18.2 - - + -
87B ASN* 1.3 72.7 + - - +
89B GLU* 1.3 66.7 + - - +
90B LEU* 4.2 2.5 - - + +
108B MET* 3.9 19.3 - - - -
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Residues in contact with GLU 89 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85A TYR 3.4 5.5 - - - +
86A LEU* 4.3 2.0 - - - +
87A ASN* 2.9 45.4 + - + +
49B ARG* 4.2 9.4 + - - -
57B LYS* 4.1 27.1 + - + +
58B TYR 3.4 5.8 - - - +
59B THR* 3.7 20.3 + - + +
87B ASN* 4.1 15.1 - - - +
88B MET* 1.3 77.9 - - - +
90B LEU* 1.3 61.1 + - - +
91B THR* 5.0 2.4 + - - +
6R C 4.7 8.7 - - - +
7R G 6.0 0.3 - - - +
8R G 4.9 2.8 + - - +
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Residues in contact with LEU 90 (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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84A SER* 4.1 7.9 - - - +
85A TYR 4.0 10.3 - - - +
86A LEU* 4.0 25.1 - - + +
122A ILE* 3.8 20.4 - - + -
56B ARG 3.8 0.5 - - - +
57B LYS* 3.2 5.5 - - - -
58B TYR* 2.8 48.5 + - + -
60B ILE* 5.8 3.6 - - + +
88B MET* 4.2 1.9 - - + -
89B GLU* 1.3 71.2 - - - +
91B THR* 1.3 60.2 + - - +
92B ILE* 3.9 25.5 + - + -
104B ILE* 3.9 19.7 - - + -
108B MET* 3.4 30.5 - - + -
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Residues in contact with THR 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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84A SER* 2.9 20.6 + - - -
85A TYR* 2.9 35.2 + - + +
51B SER* 5.4 0.2 - - - +
55B ASN* 3.6 35.4 - - + +
56B ARG 3.5 4.5 - - - +
57B LYS* 3.7 24.7 - - - +
89B GLU* 4.0 1.8 + - - +
90B LEU* 1.3 71.2 - - - +
92B ILE* 1.3 61.2 + - - +
93B PRO* 5.1 0.7 - - + -
9R A 4.4 2.8 + - - +
10R U 4.5 0.2 - - - +
11R C 3.7 26.3 + - - +
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Residues in contact with ILE 92 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A SER* 3.8 7.6 - - - +
122A ILE* 4.0 17.0 - - + -
125A ASN* 5.7 0.4 - - - +
55B ASN* 4.0 2.2 - - - -
56B ARG* 2.9 42.8 + - + +
58B TYR* 4.2 15.0 - - + -
90B LEU* 3.9 30.3 - - + +
91B THR* 1.3 78.2 - - - +
93B PRO* 1.3 72.0 - - + +
94B ILE* 3.5 0.3 + - - -
96B ALA* 3.4 31.4 - - + -
101B CYS* 4.1 15.9 - - - -
104B ILE* 4.0 16.6 - - + -
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Residues in contact with PRO 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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82A TRP* 3.4 44.2 - - + -
83A ARG 3.1 28.3 - - - +
84A SER* 4.1 1.8 - - - -
54B GLN* 3.2 13.7 - - + +
55B ASN* 3.4 13.4 - - - +
91B THR 3.9 2.9 - - - +
92B ILE* 1.3 90.5 - - + +
94B ILE* 1.3 59.4 + - - +
95B PHE* 2.9 17.5 + - + +
96B ALA* 3.1 17.5 + - - +
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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