Contacts of the helix formed by residues 97 - 113 (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 THR 97 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125A ASN* 3.8 3.8 - - - +
95B PHE 4.0 8.3 - - - +
96B ALA* 1.3 76.6 - - - +
98B ASN* 1.3 66.8 + - - +
99B SER* 3.5 15.6 + - - -
100B ASP* 2.7 26.5 + - - +
101B CYS* 2.9 21.3 + - - -
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Residues in contact with ASN 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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123A ALA 3.6 22.3 + - - +
124A ALA* 3.8 17.8 + - - +
125A ASN* 2.9 23.3 + - - +
97B THR* 1.3 74.3 - - - +
99B SER* 1.3 58.2 + - - +
101B CYS* 3.3 1.1 + - - -
102B GLU* 2.9 41.5 + - - +
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Residues in contact with SER 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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97B THR* 3.1 10.2 + - - -
98B ASN* 1.3 76.4 - - - +
100B ASP* 1.3 68.3 + - - +
102B GLU* 3.2 14.6 + - - +
103B LEU* 3.1 21.0 + - - +
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Residues in contact with ASP 100 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A LYS* 2.9 34.2 + - - +
82A TRP* 3.9 18.8 - - + -
95B PHE 4.0 1.6 - - - +
96B ALA* 3.4 16.7 - - + -
97B THR* 2.7 40.2 + - - +
99B SER* 1.3 76.7 - - - +
101B CYS* 1.3 64.1 + - - +
103B LEU* 3.3 10.2 + - - +
104B ILE* 3.1 27.4 + - - +
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Residues in contact with CYS 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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122A ILE* 3.3 29.1 - - + +
123A ALA* 4.0 5.8 - - - +
125A ASN* 3.9 21.8 - - - -
56B ARG* 5.0 0.7 - - - -
92B ILE* 4.1 19.3 - - - -
96B ALA* 4.1 15.9 - - - -
97B THR 2.9 15.5 + - - +
98B ASN* 3.6 7.6 - - - +
99B SER 3.2 0.2 - - - -
100B ASP* 1.3 74.4 - - - +
102B GLU* 1.3 65.6 + - - +
104B ILE* 3.4 9.1 + - - +
105B VAL* 3.1 28.2 + - - +
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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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123A ALA* 3.9 21.8 - - + +
98B ASN* 2.9 30.2 + - - +
99B SER* 3.2 13.9 + - - +
101B CYS* 1.3 73.6 - - - +
103B LEU* 1.3 59.1 + - - +
105B VAL* 3.2 8.6 + - - +
106B LYS* 3.0 35.8 + - + +
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Residues in contact with LEU 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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10A VAL* 3.8 26.5 - - + +
12A ASN* 4.7 10.3 - - - +
18A VAL* 5.6 1.1 - - + -
42A TYR* 3.2 26.7 - - + +
64A VAL* 4.0 20.2 - - + -
65A PRO 5.2 3.6 - - - +
99B SER 3.1 11.5 + - - +
100B ASP* 3.5 11.9 - - - +
102B GLU* 1.3 75.0 - - - +
104B ILE* 1.3 57.9 + - - +
106B LYS* 3.1 11.5 + - + +
107B ALA* 2.9 27.8 + - - +
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Residues in contact with ILE 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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64A VAL* 4.1 26.0 - - + -
82A TRP* 5.0 7.2 - - + -
84A SER* 3.3 28.3 - - - +
122A ILE* 5.3 0.7 - - + -
90B LEU* 3.9 30.7 - - + -
92B ILE* 4.0 24.0 - - + -
96B ALA* 5.1 0.7 - - + -
100B ASP* 3.1 17.6 + - + +
101B CYS* 3.6 13.5 - - - +
102B GLU 3.3 0.2 - - - -
103B LEU* 1.3 76.8 - - - +
105B VAL* 1.3 60.5 + - - +
107B ALA* 3.5 7.8 + - - +
108B MET* 3.3 30.8 + - + +
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Residues in contact with VAL 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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112A LEU* 4.7 2.5 - - + +
114A ASP* 4.9 4.0 - - - +
119A PRO* 3.9 37.9 - - + +
122A ILE* 3.9 23.8 - - + -
123A ALA* 4.3 5.6 - - + +
101B CYS 3.1 16.8 + - - +
102B GLU* 3.5 9.4 - - - +
103B LEU 3.1 0.4 - - - -
104B ILE* 1.3 75.2 - - - +
106B LYS* 1.3 66.1 + - + +
108B MET* 3.0 17.9 + - + +
109B GLN* 3.0 39.0 + - + +
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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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9A LEU 3.4 6.2 - - - +
10A VAL* 4.0 15.4 - - + -
11A ASP* 3.3 23.2 + - - +
12A ASN* 3.8 20.2 - - - +
114A ASP* 5.6 3.4 + - - -
102B GLU* 3.0 19.4 + - + +
103B LEU* 3.4 13.2 - - + +
105B VAL* 1.3 76.1 - - + +
107B ALA* 1.3 57.7 + - - +
109B GLN* 3.2 19.5 + - - +
110B GLY* 2.8 26.2 + - - -
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Residues in contact with ALA 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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9A LEU* 3.4 31.5 - - + +
10A VAL* 3.9 16.1 - - + +
62A VAL* 4.8 6.3 - - + -
64A VAL* 4.0 22.9 - - + -
103B LEU 2.9 12.7 + - - +
104B ILE 3.6 9.9 - - - +
105B VAL 3.2 0.2 - - - -
106B LYS* 1.3 75.6 - - - +
108B MET* 1.3 58.1 + - + +
110B GLY 3.4 0.5 + - - -
111B LEU* 3.0 24.6 + - - +
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Residues in contact with MET 108 (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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62A VAL* 6.3 1.1 - - + -
86A LEU* 3.7 26.9 - - + -
88A MET* 6.2 0.2 - - + -
112A LEU* 3.5 24.8 - - + +
119A PRO* 6.4 0.2 - - + -
122A ILE* 4.0 15.3 - - + -
88B MET* 3.9 25.8 - - - -
90B LEU* 3.4 32.8 - - + -
104B ILE* 3.3 22.7 - - + +
105B VAL* 3.0 25.8 + - + +
107B ALA* 1.3 76.0 - - + +
109B GLN* 1.3 64.3 + - - +
111B LEU* 3.4 8.3 + - - +
112B LEU* 3.4 25.3 + - - +
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Residues in contact with GLN 109 (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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112A LEU* 2.9 36.3 + - + +
113A LYS* 4.2 1.4 - - - +
114A ASP* 3.2 42.1 + - - +
119A PRO* 5.1 0.2 - - - +
105B VAL* 3.0 27.3 + - + +
106B LYS* 3.2 25.5 + - - +
108B MET* 1.3 75.9 - - - +
110B GLY* 1.3 63.9 + - - +
112B LEU* 3.3 4.9 + - - +
113B LYS* 3.1 23.8 + - - +
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Residues in contact with GLY 110 (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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7A PHE* 4.4 0.6 - - - -
8A VAL 4.0 9.0 - - - -
9A LEU* 3.3 22.4 - - - -
11A ASP* 5.9 2.7 - - - -
106B LYS 2.8 11.1 + - - -
109B GLN* 1.3 78.2 - - - +
111B LEU* 1.3 55.9 + - - +
112B LEU 3.2 0.7 + - - -
113B LYS* 3.4 8.1 + - - -
116B ASN* 2.5 33.1 + - - -
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Residues in contact with LEU 111 (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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7A PHE* 4.2 16.9 - - + -
9A LEU* 4.2 3.0 - - + +
44A VAL* 3.7 32.1 - - + -
60A ILE* 3.9 17.7 - - + -
62A VAL* 3.9 23.1 - - + -
86A LEU* 4.7 3.6 - - + -
88A MET* 4.6 14.8 - - + -
107B ALA 3.0 17.4 + - - +
108B MET* 3.7 6.7 - - - +
109B GLN 3.3 0.4 - - - -
110B GLY* 1.3 75.6 - - - +
112B LEU* 1.3 73.6 + - + +
113B LYS 4.0 0.2 + - - -
116B ASN* 4.3 3.8 - - - +
118B ILE* 3.9 22.1 - - + +
119B PRO* 3.3 20.6 - - - +
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Residues in contact with LEU 112 (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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60A ILE* 5.7 0.7 - - + -
88A MET* 5.2 13.7 - - + -
105A VAL* 5.9 0.9 - - + -
108A MET* 3.7 49.8 - - + +
109A GLN* 2.9 36.8 + - + +
112A LEU* 3.8 27.4 - - + -
88B MET* 6.1 1.1 - - - -
108B MET 3.4 8.0 + - - +
109B GLN* 3.3 6.4 + - - +
110B GLY 3.1 0.4 - - - -
111B LEU* 1.3 98.4 - - + +
113B LYS* 1.3 62.4 + - - +
118B ILE* 4.9 11.4 - - + -
119B PRO* 3.8 16.9 - - + +
122B ILE* 5.6 0.4 - - + -
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Residues in contact with LYS 113 (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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11A ASP* 4.9 10.7 + - - -
109A GLN* 4.3 2.5 - - - +
109B GLN 3.1 14.7 + - - +
110B GLY* 3.4 7.8 + - - +
111B LEU 3.6 0.2 - - - -
112B LEU* 1.3 78.6 - - - +
114B ASP* 1.3 75.9 + - + +
116B ASN* 3.2 31.5 + - - +
119B PRO* 3.3 8.0 - - - +
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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