Contacts of the strand formed by residues 58 - 72 (chain B) in PDB entry 5FJV
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 VAL 58 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51B VAL* 3.2 34.5 - - + +
52B PRO* 4.9 1.8 - - + -
53B ASN* 4.1 17.9 + - - +
56B ASP 4.0 0.4 - - - -
57B VAL* 1.3 72.8 - - - +
59B ILE* 1.3 62.8 + - - +
60B VAL* 4.4 2.5 - - + -
89B TRP* 3.9 28.5 - - + -
90B SER 4.8 7.0 - - - +
115B TRP* 4.1 19.7 - - + -
184B LYS 3.4 9.9 - - - +
185B ILE* 3.3 15.0 - - + +
186B ASP 3.2 21.5 + - - -
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Residues in contact with ILE 59 (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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57B VAL* 2.9 52.9 + - + +
58B VAL* 1.3 73.7 - - - +
60B VAL* 1.3 66.1 + - - +
61B ARG* 4.4 6.4 - - + +
88B GLU 3.5 8.0 - - - +
89B TRP* 3.6 12.0 - - - -
90B SER 4.6 1.2 + - - +
186B ASP* 3.4 13.5 - - + +
188B GLU* 4.0 29.8 - - + +
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Residues in contact with VAL 60 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58B VAL* 4.4 4.3 - - + -
59B ILE* 1.3 77.4 - - - +
61B ARG* 1.3 78.5 + - - +
62B PHE* 3.4 7.5 + - + +
87B GLN* 4.2 17.0 - - + +
88B GLU 3.2 15.5 - - - +
89B TRP* 4.0 14.8 - - + -
117B PRO* 3.8 20.2 - - + -
119B ILE* 5.9 1.3 - - + -
185B ILE* 3.7 30.1 - - + -
186B ASP 3.0 7.9 + - - +
187B LEU* 3.5 13.0 - - + -
188B GLU 3.0 20.8 + - - -
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Residues in contact with ARG 61 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59B ILE* 3.8 6.3 + - + +
60B VAL* 1.3 77.5 - - - +
62B PHE* 1.3 57.8 + - - +
87B GLN* 3.3 3.8 - - - -
88B GLU* 2.4 88.8 + - + +
188B GLU* 3.3 42.2 + - + +
190B MET* 3.3 46.7 - - + +
191B GLU* 3.4 21.2 + - - +
194B VAL* 5.5 1.0 - - - +
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Residues in contact with PHE 62 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60B VAL* 4.1 4.3 - - + +
61B ARG* 1.3 75.2 - - - +
63B GLY* 1.3 61.4 + - - +
85B LEU* 3.1 49.4 - - + -
86B LYS 3.5 6.3 - - - -
87B GLN* 3.8 13.2 - - + -
119B ILE* 4.2 12.1 - - + -
175B PHE* 3.3 39.7 - + + -
187B LEU* 3.7 33.9 - - + -
188B GLU 3.0 11.1 + - - +
189B GLN* 3.9 6.9 - - - +
190B MET* 3.2 20.7 + - - +
229B VAL* 4.4 12.8 - - + -
231B TYR* 3.9 21.6 + + - -
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Residues in contact with GLY 63 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62B PHE* 1.3 80.5 - - - +
64B LEU* 1.3 58.3 + - - -
84B TRP 3.4 0.5 - - - +
85B LEU* 3.5 3.9 - - - -
86B LYS* 2.5 64.8 + - - +
190B MET* 3.8 9.9 - - - -
192B GLN* 5.8 2.7 - - - -
231B TYR* 4.1 6.1 - - - -
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Residues in contact with LEU 64 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62B PHE* 6.1 0.2 - - + -
63B GLY* 1.3 72.9 - - - -
65B SER* 1.3 67.5 + - - +
66B ILE* 3.8 22.7 - - + -
83B VAL* 3.5 27.4 - - + -
84B TRP 3.5 15.0 - - - +
85B LEU* 3.7 21.3 - - + -
86B LYS* 3.6 6.9 + - - +
173B MET* 4.6 3.1 - - - -
175B PHE* 4.4 17.9 - - + -
192B GLN* 5.2 2.5 + - - +
196B LEU* 3.5 30.1 - - + +
231B TYR* 4.0 29.5 + - + -
233B PHE* 4.3 15.9 - - + -
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Residues in contact with SER 65 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220A ASP 4.7 3.1 + - - -
221A CYS* 4.8 1.4 - - - +
64B LEU* 1.3 76.6 - - - +
66B ILE* 1.3 63.2 + - - +
67B ALA 4.0 0.6 + - - -
83B VAL* 3.7 4.0 - - - -
84B TRP* 3.2 56.0 + - - +
86B LYS* 3.2 23.9 + - - +
195B ASP 2.8 20.7 + - - -
196B LEU 3.3 5.8 - - - -
198B ASP* 5.2 4.9 - - - -
199B TYR* 6.0 0.7 - - - -
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Residues in contact with ILE 66 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64B LEU* 3.8 28.7 - - + -
65B SER* 1.3 72.6 - - - +
67B ALA* 1.3 63.2 + - - +
68B GLN* 3.9 21.3 - - - +
69B LEU* 5.3 0.2 - - - -
81B THR* 5.0 7.0 - - + -
82B ASN 4.1 2.5 - - - +
83B VAL* 3.9 15.3 - - + -
84B TRP* 5.8 0.4 - - - -
173B MET* 5.7 0.2 - - - -
196B LEU* 2.6 29.4 + - + +
197B LYS* 5.1 2.9 - - + -
198B ASP* 5.5 0.2 - - - +
199B TYR* 3.6 18.7 + - - +
200B TRP* 3.7 11.2 + - + +
207B ILE* 3.9 25.6 - - + -
233B PHE* 4.1 22.4 - - + -
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Residues in contact with ALA 67 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122A TYR 5.0 3.1 - - - +
124A ASN* 3.4 4.3 - - - +
65B SER 4.0 1.8 + - - -
66B ILE* 1.3 75.4 - - - +
68B GLN* 1.3 58.7 + - - +
82B ASN* 3.0 35.9 + - - +
84B TRP* 3.6 29.7 - - + +
199B TYR* 2.9 25.0 - - + +
200B TRP* 4.6 0.4 - - - -
201B GLU* 3.2 22.0 + - + +
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Residues in contact with GLN 68 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A MET* 5.9 0.2 - - - +
124A ASN* 2.8 47.6 - - + +
156A SER* 2.7 40.8 + - - -
66B ILE* 3.5 10.6 - - - +
67B ALA* 1.3 77.8 - - - +
69B LEU* 1.3 67.4 + - - +
70B ILE* 3.1 23.0 - - + +
81B THR* 3.8 1.0 - - - +
82B ASN* 2.7 35.2 + - + +
200B TRP* 5.1 1.3 - - - -
201B GLU* 4.5 17.9 - - + +
203B GLY* 4.3 4.6 - - - -
204B GLU* 3.4 24.9 + - - -
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Residues in contact with LEU 69 (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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66B ILE* 4.6 1.0 - - - +
68B GLN* 1.3 86.0 + - - +
70B ILE* 1.3 65.2 + - - +
71B ASP* 4.7 7.0 - - - +
72B VAL* 6.1 1.8 - - + -
79B MET* 4.1 16.8 - - + -
80B THR 3.4 10.1 - - - +
81B THR* 3.3 28.0 - - + -
200B TRP* 4.7 5.8 - - - +
201B GLU 5.0 0.4 + - - -
202B SER 5.5 0.9 - - - +
203B GLY* 5.5 0.3 - - - -
204B GLU* 3.5 7.6 + - - +
205B TRP* 4.0 18.0 + - + +
207B ILE* 3.5 44.2 - - + -
235B ILE* 3.5 26.9 - - + -
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Residues in contact with ILE 70 (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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78A MET* 4.5 12.3 - - + +
124A ASN* 3.8 5.2 - - + -
126A ASP* 3.2 42.8 - - + +
156A SER* 5.3 0.2 - - - -
68B GLN* 3.1 41.7 + - + +
69B LEU* 1.3 75.3 - - - +
71B ASP* 1.3 69.0 + - + +
80B THR* 2.9 34.6 + - + +
81B THR 4.4 0.9 - - - +
82B ASN* 4.3 15.9 - - + +
152B ILE* 5.0 3.4 - - + -
204B GLU* 3.6 20.4 - - - +
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Residues in contact with ASP 71 (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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78A MET* 6.2 1.3 - - + -
69B LEU* 3.5 5.4 - - - +
70B ILE* 1.3 89.2 - - + +
72B VAL* 1.3 89.4 + - - +
73B ASP* 3.0 26.8 + - - +
79B MET* 3.4 3.6 - - - +
80B THR* 2.5 45.7 + - - +
205B TRP* 5.7 1.2 - - - -
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Residues in contact with VAL 72 (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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69B LEU* 6.1 2.5 - - + -
71B ASP* 1.3 95.6 + - - +
73B ASP* 1.3 68.2 + - - +
74B GLU* 3.9 9.6 - - - +
78B MET 3.6 7.2 - - - +
79B MET* 4.2 7.2 - - + +
159B ILE 5.4 1.1 - - - +
160B ASP* 4.9 16.6 - - + +
169B GLN* 5.6 0.2 - - + -
171B CYS* 5.5 5.4 - - - -
205B TRP* 2.9 47.9 - - + -
235B ILE* 4.2 21.1 - - + -
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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