Contacts of the strand formed by residues 76 - 91 (chain B) in PDB entry 4EC7
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 SER 76 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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60B ASN* 4.6 3.1 + - - -
64B SER 3.5 8.2 + - - +
65B GLY* 3.1 18.9 - - - -
66B CYS* 2.7 37.9 + - - +
69B ILE* 3.8 29.0 - - - +
74B TRP 4.1 0.2 + - - -
75B ASN* 1.3 77.7 - - - +
77B TYR* 1.3 67.8 + - - +
109B VAL 3.1 9.4 - - - -
110B ILE* 3.9 0.9 - - - -
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Residues in contact with TYR 77 (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 GLU* 2.8 37.5 + - - -
59B PRO* 3.3 18.8 - - + +
60B ASN* 4.4 9.2 - - - +
65B GLY* 4.8 0.4 - - - -
66B CYS* 3.4 9.4 - - - +
75B ASN 5.7 0.7 - - - -
76B SER* 1.3 79.8 - - - +
78B CYS* 1.3 60.8 + - - +
79B THR* 2.8 31.2 + - + +
109B VAL* 2.8 55.2 + - + +
111B THR* 5.5 4.7 - - + -
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Residues in contact with CYS 78 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B VAL* 4.9 0.7 - - - -
14B CYS* 1.8 78.9 - - + -
56B CYS* 3.8 7.2 - - - -
58B ASN 4.2 1.6 - - - +
59B PRO* 2.7 30.6 + - - +
66B CYS* 3.8 0.7 - - - -
77B TYR* 1.3 70.9 - - - +
79B THR* 1.3 65.1 + - - +
106B CYS* 3.6 8.3 - - - -
107B VAL* 3.1 25.4 - - - +
108B CYS* 3.4 16.2 - - - -
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Residues in contact with THR 79 (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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56B CYS* 3.3 9.6 - - - -
77B TYR* 2.8 36.5 + - + +
78B CYS* 1.3 71.4 + - - +
80B GLU* 1.3 86.9 + - - +
107B VAL* 2.9 34.4 + - - +
109B VAL* 4.7 8.1 - - - -
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Residues in contact with GLU 80 (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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54B THR 4.2 0.9 - - - +
55B LYS* 3.8 15.3 + - - +
56B CYS* 3.1 42.9 + - - +
79B THR* 1.3 95.8 - - - +
81B THR* 1.3 61.7 - - - +
82B ASP* 5.2 0.9 - - - +
103B GLU* 3.5 45.1 - - + +
105B ALA 3.1 7.9 - - - +
107B VAL* 5.3 0.2 - - - +
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Residues in contact with THR 81 (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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104A THR 4.8 2.2 + - - -
105A ALA* 4.2 10.0 - - + +
80B GLU* 1.3 78.6 - - - +
82B ASP* 1.3 67.1 + - - +
103B GLU* 3.2 4.7 - - - -
104B THR* 2.8 28.8 + - - -
105B ALA* 2.9 26.8 + - - +
107B VAL* 3.8 31.4 - - + -
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Residues in contact with ASP 82 (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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52A PHE* 4.1 13.2 - - - -
54A THR* 5.6 0.2 + - - -
104A THR* 5.2 2.9 + - - +
80B GLU* 5.2 0.9 - - - +
81B THR* 1.3 78.7 - - - +
83B THR* 1.3 67.0 + - - +
84B PHE* 4.8 4.7 - - + -
101B ARG* 3.2 46.3 + - + +
102B ILE 3.2 3.1 + - - +
103B GLU* 3.4 29.6 + - - +
104B THR* 3.6 4.1 + - - -
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Residues in contact with THR 83 (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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52A PHE* 3.9 24.1 + - - +
83A THR* 4.6 6.7 - - - +
85A ILE* 4.9 3.4 - - + +
104A THR* 3.7 15.0 + - - -
82B ASP* 1.3 74.2 - - - +
84B PHE* 1.3 73.0 + - - +
85B ILE* 3.7 29.2 - - + +
101B ARG* 3.3 8.3 - - - +
102B ILE* 2.7 35.8 + - + +
104B THR* 3.4 28.0 + - + -
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Residues in contact with PHE 84 (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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20A TRP* 3.7 23.6 - + + -
52A PHE* 3.6 54.4 + + + +
85A ILE* 5.3 3.6 - - - +
29B ILE* 3.5 35.9 - - + -
82B ASP* 4.8 5.2 - - + -
83B THR* 1.3 86.3 + - - +
85B ILE* 1.3 63.8 + - - +
99B PHE* 4.0 15.6 - - + -
100B ILE 3.3 5.4 - - - +
101B ARG* 3.6 51.8 - - + -
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Residues in contact with ILE 85 (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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83A THR* 4.9 4.0 - - - +
84A PHE 5.0 4.5 - - - +
85A ILE* 4.1 33.4 - - + -
86A LYS* 5.9 3.1 - - + +
51B PHE* 4.0 28.7 - - + -
52B PHE 4.9 5.8 - - - +
83B THR* 3.7 24.2 - - + -
84B PHE* 1.3 79.1 - - - +
86B LYS* 1.3 74.3 + - - +
87B ALA 3.3 1.0 + - - -
99B PHE* 3.9 3.1 - - - -
100B ILE* 2.8 35.3 + - + +
102B ILE* 4.1 22.9 - - + -
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Residues in contact with LYS 86 (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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86A LYS* 6.1 0.2 - - - +
200A L44 3.2 104.4 - - + +
49B GLU* 4.8 0.2 - - - +
51B PHE* 4.8 1.9 - - - -
85B ILE* 1.3 80.0 - - - +
87B ALA* 1.3 61.3 + - - +
97B TRP* 4.1 33.2 - - + -
98B ARG* 3.6 8.5 - - - +
99B PHE* 3.7 40.7 - - + -
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Residues in contact with ALA 87 (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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36B VAL* 4.2 6.7 - - + -
49B GLU* 3.4 12.6 - - - +
51B PHE* 3.6 16.2 - - + -
85B ILE 3.3 1.6 + - - -
86B LYS* 1.3 74.8 - - - +
88B LEU* 1.3 61.9 + - - +
89B THR* 3.6 3.7 + - + +
97B TRP* 3.4 7.9 - - - -
98B ARG 3.0 31.2 + - - +
100B ILE* 3.5 33.7 - - + -
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Residues in contact with LEU 88 (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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36B VAL* 3.7 2.4 - - - +
37B MET* 2.9 43.1 + - + +
39B ASN 4.1 13.2 - - - +
40B VAL* 3.9 27.6 - - + -
41B ASN 5.0 2.5 - - - +
49B GLU* 2.5 22.9 + - - +
87B ALA* 1.3 70.4 - - - +
89B THR* 1.3 61.0 + - - +
95B ALA* 4.6 9.0 - - + -
96B SER* 3.7 16.8 - - - +
97B TRP* 3.4 42.0 - - + +
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Residues in contact with THR 89 (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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34B VAL* 3.9 25.5 - - + +
35B THR 3.3 14.1 - - - +
36B VAL* 5.0 2.5 - - - -
37B MET* 4.2 2.0 - - - +
87B ALA* 3.7 15.5 - - + +
88B LEU* 1.3 77.7 - - - +
90B MET* 1.3 61.6 + - - +
95B ALA* 3.2 7.1 - - - +
96B SER* 2.7 54.1 + - - +
98B ARG* 3.9 26.2 + - + -
100B ILE* 4.3 9.2 - - + -
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Residues in contact with MET 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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34B VAL* 3.9 7.7 - - - +
35B THR* 3.0 49.3 + - + +
36B VAL 4.5 1.3 - - - +
37B MET* 3.7 43.3 - - + +
38B GLU 5.5 0.4 - - - -
89B THR* 1.3 80.3 - - - +
91B GLU* 1.3 65.9 + - - +
92B GLY* 3.9 22.2 - - - +
94B GLN 3.6 9.6 - - - +
95B ALA* 4.6 2.5 - - - -
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Residues in contact with GLU 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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34B VAL* 4.6 6.1 - - + +
35B THR* 4.9 3.4 - - + -
90B MET* 1.3 75.5 - - - +
92B GLY* 1.3 62.5 + - - +
93B ASN* 3.4 5.7 + - - +
94B GLN* 3.4 25.1 + - + +
96B SER* 6.1 0.4 - - - +
98B ARG* 3.8 31.6 + - - +
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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