Contacts of the strand formed by residues 97 - 114 (chain V) in PDB entry 4EDW
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 ALA 97 (chain V).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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39V LEU* 4.6 9.0 - - + -
90V LEU* 4.3 16.8 - - + -
91V THR 3.6 9.9 - - - +
92V MET* 4.5 7.5 - - - -
95V LYS 4.1 1.0 + - - -
96V GLN* 1.3 87.7 + - - +
98V ALA* 1.3 59.9 + - - +
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Residues in contact with ALA 98 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90V LEU* 3.7 5.8 - - - +
91V THR* 2.8 51.0 + - - +
93V ASP* 3.7 16.6 - - - +
97V ALA* 1.3 76.2 - - - +
99V TRP* 1.3 59.5 + - - +
100V ARG* 3.3 33.6 + - + +
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Residues in contact with TRP 99 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42V VAL* 3.7 22.0 - - + -
51V GLN* 4.2 1.8 - - - -
88V LYS* 3.2 72.5 + - + +
89V ALA* 3.5 6.3 - - - -
90V LEU* 3.4 44.0 - - + +
98V ALA* 1.3 67.5 - - - +
100V ARG* 1.4 60.6 + - - +
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Residues in contact with ARG 100 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30V ASP* 4.1 26.0 + - + -
31V ILE* 6.5 0.4 - - + -
32V LYS* 3.9 30.1 - - - +
36V VAL* 5.2 5.4 - - + -
88V LYS* 3.4 7.8 - - - +
89V ALA* 2.8 34.5 + - - +
91V THR* 3.9 21.5 - - + +
93V ASP* 3.0 34.2 + - - +
98V ALA* 3.5 20.7 - - + +
99V TRP* 1.4 77.2 - - - +
101V PHE* 1.4 64.3 + - - +
102V ILE* 3.6 3.0 + - + +
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Residues in contact with PHE 101 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30V ASP* 3.4 7.4 - - - +
31V ILE* 3.2 49.4 + - + +
86V PHE* 3.8 36.6 - + + -
87V VAL* 3.5 10.1 - - - -
88V LYS* 3.6 43.3 - - + +
100V ARG* 1.4 70.6 - - - +
102V ILE* 1.3 60.2 + - - +
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Residues in contact with ILE 102 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25V LYS* 3.8 14.6 - - + -
28V ALA* 3.7 31.0 - - + -
29V THR 3.8 3.8 - - - +
30V ASP* 4.6 7.0 - - + -
36V VAL* 4.5 7.2 - - + -
38V VAL* 4.1 2.7 - - + -
53V PHE* 4.1 7.0 - - + -
85V THR 3.5 0.7 - - - +
86V PHE* 3.2 9.6 - - - -
87V VAL* 2.8 43.7 + - - +
89V ALA* 3.7 20.4 - - + -
91V THR* 3.9 26.9 - - + -
100V ARG* 4.1 5.8 - - + +
101V PHE* 1.3 77.5 - - - +
103V ARG* 1.3 58.1 + - - +
104V ILE* 3.8 21.3 + - + -
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Residues in contact with ARG 103 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25V LYS* 5.2 0.5 + - - -
28V ALA* 4.3 10.2 - - - +
29V THR* 3.0 47.0 + - - +
30V ASP 3.2 23.2 + - - -
31V ILE 4.3 9.3 + - - -
33V GLY* 4.6 8.1 - - - +
84V HIS* 3.7 37.2 - - + -
85V THR 3.5 5.8 - - - +
86V PHE* 3.6 35.1 - - + -
102V ILE* 1.3 71.4 - - - +
104V ILE* 1.4 63.9 + - - +
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Residues in contact with ILE 104 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25V LYS* 3.6 32.1 - - + +
53V PHE* 4.2 14.6 - - + -
54V PHE 3.5 24.5 - - - +
55V GLU* 3.8 15.0 - - + +
84V HIS* 3.2 8.3 - - - +
85V THR* 2.9 51.0 + - + +
87V VAL* 3.7 23.6 - - + -
102V ILE* 3.8 18.6 - - + +
103V ARG* 1.4 79.6 - - - +
105V ASP* 1.4 61.8 + - - +
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Residues in contact with ASP 105 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54V PHE 4.2 1.7 - - - +
55V GLU* 3.3 32.9 - - + +
56V THR 3.2 29.4 + - - +
57V LYS* 3.7 23.2 + - + +
82V THR* 3.5 14.2 - - + +
83V THR 3.8 5.4 - - - -
84V HIS* 3.2 22.8 + - - -
104V ILE* 1.4 71.7 - - - +
106V THR* 1.3 58.2 + - - +
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Residues in contact with THR 106 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99H TYR* 3.5 10.7 - - - -
54V PHE 5.4 3.2 + - - -
56V THR* 3.3 20.6 + - - +
83V THR* 2.9 9.2 + - - +
84V HIS* 3.5 25.1 - - - +
85V THR* 3.4 31.7 - - - +
104V ILE 3.4 0.4 + - - -
105V ASP* 1.3 74.1 + - - +
107V ALA* 1.3 72.8 + - + +
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Residues in contact with ALA 107 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99H TYR* 3.7 18.6 - - + +
56V THR* 3.3 9.0 + - - +
57V LYS* 4.3 0.2 - - - -
82V THR* 3.2 13.3 + - - +
83V THR* 3.0 39.4 + - - +
106V THR* 1.3 88.1 - - + +
108V CYS* 1.3 61.2 + - - +
109V VAL* 4.3 11.0 - - + -
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Residues in contact with CYS 108 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99H TYR* 3.2 14.1 + - - -
15V CYS* 3.7 31.3 - - + +
16V ASP 3.7 7.0 - - - -
17V SER* 3.9 17.3 - - - -
58V CYS* 2.0 59.7 - - - +
80V CYS* 3.7 5.8 - - - -
81V THR 3.4 3.8 - - - -
107V ALA* 1.3 74.7 - - - +
109V VAL* 1.3 62.1 + - - +
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Residues in contact with VAL 109 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99H TYR* 5.3 0.4 - - - +
15V CYS* 3.7 5.2 - - - -
80V CYS* 3.4 0.5 - - - -
81V THR* 2.7 47.6 + - + +
83V THR* 3.6 28.7 - - + +
107V ALA* 4.1 16.1 - - + -
108V CYS* 1.3 79.1 - - - +
110V CYS* 1.4 64.4 + - - +
111V VAL* 4.7 6.7 - - + -
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Residues in contact with CYS 110 (chain V).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14V VAL* 3.6 17.5 - - + +
15V CYS* 3.6 10.8 - - - -
68V CYS* 2.0 46.4 - - - -
71V ILE* 3.9 14.6 - - + -
78V SER* 3.8 12.6 - - - -
79V TYR 3.5 4.3 - - - -
109V VAL* 1.4 74.8 - - - +
111V VAL* 1.3 64.9 + - - +
112V LEU* 4.2 6.0 + - - +
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Residues in contact with VAL 111 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78V SER* 3.3 6.9 - - - -
79V TYR* 3.1 66.1 + - + +
81V THR* 3.9 21.5 - - + -
109V VAL* 4.7 7.2 - - + -
110V CYS* 1.3 76.9 - - - +
112V LEU* 1.3 69.1 + - - +
113V SER* 6.2 0.2 - - - -
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Residues in contact with LEU 112 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71V ILE* 3.8 28.9 - - + -
76V TRP* 3.8 38.8 - - + +
77V ASN 3.5 3.6 - - - +
78V SER* 3.7 22.9 - - - -
110V CYS* 4.2 6.1 - - - +
111V VAL* 1.3 81.6 - - - +
113V SER* 1.3 62.7 + - - +
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Residues in contact with SER 113 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76V TRP* 3.7 10.4 - - - -
77V ASN* 2.9 47.3 + - - +
78V SER* 5.7 0.4 - - - -
79V TYR* 6.0 7.9 - - - -
112V LEU* 1.3 74.4 - - - +
114V ARG* 1.3 68.5 + - - +
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Residues in contact with ARG 114 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75V HIS 4.6 1.3 - - - -
76V TRP* 4.2 23.1 - - + -
77V ASN* 3.5 9.5 + - - -
113V SER* 1.3 80.0 + - - +
115V LYS* 1.4 64.4 + - - +
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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