Contacts of the strand formed by residues 97 - 111 (chain B) in PDB entry 1O0M
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 TYR 97 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23B SER 4.3 6.2 - - - +
26B CYS* 3.6 21.7 - - + +
27B ASN* 2.7 32.2 + - - +
30B MET* 3.6 42.6 - - + +
35B LEU 3.8 4.0 + - - -
36B THR* 3.8 3.5 - - + +
40B CYS* 3.6 11.2 - - + +
41B LYS 2.7 42.4 + - - -
42B PRO 4.0 2.2 - - - -
84B CYS* 4.2 2.9 - - + -
85B ARG 3.6 11.4 - - - +
86B GLU* 3.5 26.2 - - + -
87B THR* 3.8 7.5 - - - +
95B CYS* 3.6 24.0 - - + -
96B ALA* 1.3 78.4 - - - +
98B LYS* 1.3 62.5 + - - +
99B THR* 3.9 2.1 + - - -
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Residues in contact with LYS 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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23B SER* 5.5 1.1 - - - -
26B CYS* 4.4 0.4 - - - -
83B ASP 3.4 6.9 - - - +
84B CYS* 3.7 2.3 - - - -
85B ARG* 2.9 36.5 + - + +
87B THR* 4.0 11.3 - - + +
97B TYR* 1.3 72.5 - - - +
99B THR* 1.3 80.6 + - - +
100B THR* 3.4 19.5 + - - +
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Residues in contact with THR 99 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B ALA* 3.6 31.9 - - + -
22B SER 4.1 4.9 - - - +
23B SER* 3.3 28.4 + - - +
25B TYR* 4.0 6.7 - - + -
26B CYS* 3.1 33.6 + - - +
82B THR* 3.6 10.8 - - + -
97B TYR 3.9 0.8 + - - -
98B LYS* 1.3 90.0 + - - +
100B THR* 1.3 65.1 + - - +
101B GLN* 4.9 2.6 - - + +
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Residues in contact with THR 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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82B THR* 4.4 2.0 - - - -
83B ASP* 2.8 52.7 + - + +
98B LYS* 3.4 22.6 + - - +
99B THR* 1.3 78.5 + - - +
101B GLN* 1.3 73.9 + - - +
102B ALA* 3.9 2.4 + - + -
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Residues in contact with GLN 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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19B ALA* 3.0 29.5 - - + +
20B ALA* 3.0 45.8 + - + +
21B SER 4.2 5.5 + - - -
81B ILE 3.7 7.0 - - - +
82B THR* 4.5 1.6 - - - +
99B THR* 4.4 2.4 + - + -
100B THR* 1.3 83.6 - - - +
102B ALA* 1.3 64.6 + - - +
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Residues in contact with ALA 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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80B SER* 3.7 1.9 + - - -
81B ILE* 2.9 48.1 + - + +
83B ASP* 4.5 9.4 - - - +
100B THR* 4.7 2.9 - - + +
101B GLN* 1.3 77.3 - - - +
103B ASN* 1.3 72.3 + - - +
104B LYS* 4.1 23.6 - - - -
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Residues in contact with ASN 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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78B THR* 4.1 19.4 + - - +
79B MET 3.2 5.3 - - - +
80B SER* 3.5 25.5 + - - -
102B ALA* 1.3 79.6 - - - +
104B LYS* 1.3 66.1 + - - +
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Residues in contact with LYS 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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78B THR* 3.7 7.6 - - - -
79B MET* 2.7 37.7 + - - +
81B ILE* 4.3 6.1 - - + +
83B ASP* 4.6 8.7 + - - -
102B ALA* 4.1 19.6 - - + +
103B ASN* 1.3 84.1 - - - +
105B HIS* 1.3 68.3 + - - +
106B ILE* 3.7 4.2 + - - +
123B SER* 3.7 28.0 + - - +
124B VAL* 3.1 21.5 - - - +
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Residues in contact with HIS 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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74B GLN* 3.8 15.2 + - + -
75B SER* 2.9 32.0 + - - +
76B TYR 3.0 22.3 + - - -
77B SER* 3.4 8.5 + - - -
78B THR* 3.5 23.7 - - + +
104B LYS* 1.3 73.1 - - - +
106B ILE* 1.3 60.6 + - - +
123B SER* 3.1 5.4 - - - -
124B VAL* 2.8 62.0 + - + +
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Residues in contact with ILE 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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8B PHE* 5.5 0.4 - - + -
47B VAL* 4.5 11.2 - - + -
54B VAL* 4.2 18.6 - - + -
57B VAL* 4.3 9.0 - - + -
73B TYR 3.6 1.2 - - - +
74B GLN* 3.2 2.4 - - - -
75B SER* 2.9 42.9 + - - +
79B MET* 3.6 26.9 - - + -
81B ILE* 4.0 23.3 - - + -
104B LYS 3.7 4.0 + - - +
105B HIS* 1.3 78.1 - - - +
107B ILE* 1.3 62.0 + - - +
108B VAL* 4.2 19.3 - - + -
120B PHE* 3.9 26.9 - - + -
122B ALA 3.6 3.4 - - - -
123B SER* 4.9 2.0 - - - -
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Residues in contact with ILE 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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63B VAL* 3.8 26.0 - - + -
64B ALA 5.1 1.3 - - - +
72B CYS* 4.1 8.7 - - + -
73B TYR 3.2 8.7 - - - +
74B GLN* 3.8 21.5 - - + +
106B ILE* 1.3 79.4 - - - +
108B VAL* 1.3 66.6 + - - +
120B PHE* 3.8 1.4 - - - -
121B ASP* 2.8 41.1 + - + +
122B ALA* 2.7 29.5 + - + +
124B VAL* 4.0 30.7 - - + -
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Residues in contact with VAL 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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8B PHE* 3.9 24.2 - - + -
54B VAL 5.2 0.2 - - - +
57B VAL* 3.9 16.8 - - + -
71B ASN 3.9 0.3 - - - +
72B CYS* 3.2 6.3 - - - -
73B TYR* 2.8 40.0 + - - +
106B ILE* 4.2 18.6 - - + -
107B ILE* 1.3 81.2 - - - +
109B ALA* 1.3 60.2 + - - +
110B CYS* 3.9 19.6 + - - -
117B PRO* 4.0 18.8 - - + -
119B HIS 3.2 13.9 - - - +
120B PHE* 4.2 7.4 - - + -
121B ASP 4.3 0.7 - - - +
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Residues in contact with ALA 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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65B CYS* 4.5 2.0 - - - -
69B GLN* 5.6 1.6 - - - +
71B ASN* 3.4 20.9 - - - +
72B CYS* 3.8 12.7 - - - -
108B VAL* 1.3 73.2 - - - +
110B CYS* 1.3 59.9 + - - +
117B PRO* 3.3 4.9 - - - +
118B VAL* 2.8 32.6 + - + -
119B HIS* 2.9 38.1 + - + -
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Residues in contact with CYS 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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58B CYS* 2.0 55.2 - - - -
71B ASN* 2.9 32.9 + - - +
73B TYR* 3.8 11.0 - - + -
108B VAL* 3.9 13.0 - - - -
109B ALA* 1.3 79.9 - - - +
111B GLU* 1.3 64.0 + - - +
115B TYR* 3.5 28.3 - - + +
116B VAL 3.2 4.5 - - - +
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Residues in contact with GLU 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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4B ALA* 4.3 9.2 - - - +
69B GLN* 5.3 2.3 - - - +
71B ASN* 4.1 10.6 + - - +
110B CYS* 1.3 77.3 - - - +
112B GLY* 1.3 64.0 + - - +
114B PRO 3.5 1.9 - - - +
115B TYR* 3.7 13.3 - - - -
116B VAL* 3.1 28.6 + - - +
118B VAL* 3.5 36.4 - - + +
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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