Contacts of the strand formed by residues 103 - 119 (chain B) in PDB entry 5HK5
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 ASN 103 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97B PHE 3.5 0.5 - - - +
98B ILE* 3.4 3.8 - - - -
99B ASP* 3.0 44.4 + - - +
101B ALA* 4.1 17.1 - - - +
102B ASN* 1.3 79.2 - - - +
104B VAL* 1.3 62.8 + - - +
105B VAL* 3.6 15.0 + - + +
61G VAL* 4.2 21.3 - - + +
63G THR 3.6 7.2 - - - +
64G GLU* 3.7 20.7 - - - +
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Residues in contact with VAL 104 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B ILE* 4.7 7.9 - - + -
96B LEU* 3.9 31.0 - - + -
97B PHE 3.4 7.0 - - - +
98B ILE* 5.1 5.4 - - + -
102B ASN 3.8 0.2 + - - -
103B ASN* 1.3 71.5 - - - +
105B VAL* 1.3 64.6 + - - +
61G VAL* 4.0 1.6 - - - +
62G VAL* 3.1 28.8 + - + -
63G THR* 2.7 38.6 + - + +
64G GLU 3.9 0.2 - - - -
65G ARG* 3.9 16.8 - - + +
68G LEU* 3.8 32.1 - - + -
104G PHE* 5.4 1.3 - - + -
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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
----------------------------------------------------------
96B LEU* 3.3 7.5 - - - -
97B PHE* 2.7 66.9 + - + +
99B ASP* 3.9 15.0 - - + +
103B ASN* 3.7 22.7 - - + +
104B VAL* 1.3 82.3 - - - +
106B TYR* 1.3 64.1 + - - +
107B LYS 4.1 0.2 - - - -
59G ALA* 3.3 32.3 - - + -
60G LEU 3.5 7.2 - - - +
61G VAL* 4.5 12.1 - - + -
62G VAL* 4.7 0.2 - - - -
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Residues in contact with TYR 106 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94B SER* 3.4 36.1 + - - -
95B ILE 3.5 10.1 - - - -
96B LEU* 3.7 15.0 - - + -
105B VAL* 1.3 72.8 - - - +
107B LYS* 1.3 61.7 + - - +
108B GLN* 5.8 0.4 - - + -
58G GLU 4.2 1.7 - - - +
59G ALA* 3.9 0.3 - - - -
60G LEU* 2.9 49.4 + - + +
62G VAL* 3.8 14.1 - - + +
106G ILE* 3.9 21.3 - - + -
114G GLU* 3.8 23.3 - - - -
115G ASP 4.0 13.0 + - - -
116G SER 4.7 0.7 + - - -
117G PHE* 3.5 41.4 - + + +
161G ASN* 5.6 0.3 + - - -
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Residues in contact with LYS 107 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94B SER* 3.4 4.6 - - - -
95B ILE 2.9 31.3 + - - +
97B PHE* 3.8 23.2 - - + -
105B VAL* 4.1 0.8 - - + -
106B TYR* 1.3 77.2 - - - +
108B GLN* 1.3 68.7 + - - +
109B TYR* 3.7 23.3 + - + -
50G LYS* 6.2 1.8 - - - +
55G SER* 3.9 36.5 + - - +
57G GLN* 3.7 21.7 + - + +
58G GLU 4.2 9.4 - - - +
59G ALA* 3.8 22.4 - - - +
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Residues in contact with GLN 108 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92B PRO* 3.4 26.0 - - + +
93B ILE 3.6 5.8 - - - +
94B SER* 3.6 21.4 + - - +
106B TYR* 5.8 0.6 - - - -
107B LYS* 1.3 76.7 - - - +
109B TYR* 1.3 62.4 + - - +
110B GLU* 3.2 10.4 - - - +
55G SER* 2.9 23.6 + - - -
57G GLN* 2.4 44.5 + - + +
58G GLU 5.3 0.8 + - - -
114G GLU* 6.2 2.0 - - - +
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Residues in contact with TYR 109 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92B PRO* 3.1 21.5 - - - +
93B ILE 2.8 14.8 + - - +
95B ILE* 3.8 23.3 - - + -
97B PHE* 3.5 31.2 - + - -
107B LYS* 3.7 30.1 + - + +
108B GLN* 1.3 74.3 - - - +
110B GLU* 1.3 64.2 + - - +
112B MET* 3.6 20.8 - - + +
64D ASN* 4.0 3.4 - - - +
49G ILE* 3.4 28.1 + - + +
50G LYS* 4.9 1.7 + - - -
53G LEU* 3.5 36.3 + - + -
54G ALA 3.6 15.9 - - - -
55G SER* 3.8 15.0 - - - -
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Residues in contact with GLU 110 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92B PRO* 3.3 21.8 - - - +
108B GLN* 3.2 11.4 + - - +
109B TYR* 1.3 74.1 - - - +
111B ASP* 1.3 78.9 + - - +
112B MET* 3.3 2.3 + - - +
64D ASN* 2.7 31.7 + - - +
54G ALA 4.6 3.5 + - - +
55G SER* 5.0 5.8 + - - +
57G GLN* 3.1 31.1 + - + +
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Residues in contact with ASP 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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90B LEU* 3.8 35.5 + - + +
91B SER 3.9 7.9 + - - -
92B PRO 4.6 0.2 - - - -
110B GLU* 1.3 82.7 - - - +
112B MET* 1.3 57.9 + - - +
113B VAL 3.7 1.1 - - - -
63D THR* 4.1 31.5 - - + +
64D ASN* 3.5 5.5 + - + +
65D HIS* 2.8 29.6 + - - +
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Residues in contact with MET 112 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28B PHE* 4.5 1.1 - - + -
43B TYR* 2.8 40.9 + - + +
45B ALA* 3.4 9.4 - - - +
91B SER 3.1 3.2 + - - -
93B ILE* 3.7 42.4 - - + +
95B ILE* 4.0 17.0 - - + -
109B TYR* 3.6 22.2 - - + +
110B GLU 3.5 9.4 - - - +
111B ASP* 1.3 77.2 - - - +
113B VAL* 1.3 60.8 + - - +
114B VAL 4.2 0.2 - - - -
64D ASN* 3.5 29.2 - - - -
65D HIS* 3.5 10.4 - - - +
68D ILE* 3.8 19.3 - - + -
53G LEU* 4.3 8.5 - - + -
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Residues in contact with VAL 113 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43B TYR* 3.6 5.2 - - + -
44B GLU 3.6 26.0 - - - +
45B ALA 3.6 2.5 - - - -
46B PHE* 4.0 11.9 - - + -
90B LEU* 3.0 9.2 - - - -
91B SER* 2.8 49.6 + - - +
92B PRO 4.8 0.4 - - - +
93B ILE* 3.5 27.8 - - + -
112B MET* 1.3 82.8 - - - +
114B VAL* 1.3 74.1 + - - +
115B GLU* 3.4 8.2 + - - +
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Residues in contact with VAL 114 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B ARG* 2.8 44.9 + - + -
45B ALA 2.9 12.3 + - - +
46B PHE* 3.7 15.7 - - + +
47B HIS* 4.4 2.9 - - - -
48B CYS* 3.7 17.0 - - - -
87B PRO* 3.6 18.8 - - + -
89B ARG 4.0 3.8 - - - -
90B LEU* 4.1 3.4 - - + -
112B MET 4.2 0.2 - - - -
113B VAL* 1.3 71.5 - - - +
115B GLU* 1.3 55.0 + - - +
116B SER 3.7 20.0 - - - +
117B CYS* 4.0 0.9 - - - -
65D HIS* 3.3 37.9 - - + +
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Residues in contact with GLU 115 (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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21B ARG* 3.6 24.8 + - - +
89B ARG* 2.9 53.0 + - - +
90B LEU 4.2 0.2 - - - -
91B SER* 2.5 42.5 + - - +
113B VAL* 3.4 7.8 + - - +
114B VAL* 1.3 76.2 - - - +
116B SER* 1.3 63.5 + - - +
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Residues in contact with SER 116 (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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21B ARG* 4.9 4.0 - - - +
87B PRO* 3.5 6.1 - - - +
88B THR* 2.9 39.0 + - - -
89B ARG* 3.3 24.1 + - - +
114B VAL* 3.7 5.0 - - - +
115B GLU* 1.3 80.6 - - - +
117B CYS* 1.3 66.3 + - - +
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Residues in contact with CYS 117 (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 CYS* 4.0 14.1 - - - -
20B SER* 3.7 9.6 - - - -
21B ARG* 3.5 30.6 - - - +
48B CYS* 2.1 53.8 - - + -
60B LEU* 2.7 21.4 - - - +
86B VAL 3.4 4.9 - - - -
88B THR* 3.7 8.5 + - - -
114B VAL* 4.0 1.6 - - - -
116B SER* 1.3 77.5 - - - +
118B GLY* 1.3 52.8 + - - +
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Residues in contact with GLY 118 (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 CYS* 3.7 9.2 - - - -
60B LEU* 2.1 38.4 - - - -
84B CYS 3.3 2.6 - - - +
85B CYS* 3.5 0.2 - - - -
86B VAL* 3.0 35.0 + - - +
88B THR* 3.5 9.6 - - - +
117B CYS* 1.3 66.0 - - - +
119B CYS* 1.3 58.8 + - - -
120B ARG* 3.6 0.7 + - - -
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Residues in contact with CYS 119 (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 CYS* 3.9 11.0 - - - -
51B LEU 4.5 0.2 - - - -
52B CYS* 2.0 50.5 - - - -
56B LEU* 4.4 16.2 - - + -
60B LEU* 2.6 26.0 - - + +
62B PRO* 4.0 7.4 - - - +
66B ALA* 3.5 14.0 - - + +
83B THR* 3.5 13.2 - - - +
84B CYS 3.5 4.5 - - - -
118B GLY* 1.3 70.1 - - - -
120B ARG* 1.3 71.8 + - - +
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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
------------------------------------------------------------
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