Contacts of the strand formed by residues 58 - 73 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51C VAL* 3.0 35.9 - - + -
52C PRO* 4.4 8.3 - - + +
53C ASN* 3.5 19.1 - - + +
57C VAL* 1.3 71.5 - - - +
59C ILE* 1.3 62.4 + - - +
60C VAL* 3.8 15.2 + - + -
89C TRP* 4.7 9.2 - - + -
90C SER 5.1 6.7 - - - +
115C TRP* 4.3 12.8 - - + -
184C LYS 3.1 4.6 + - - +
185C ILE* 3.1 17.8 - - + +
186C ASP* 2.7 33.4 + - - +
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Residues in contact with ILE 59 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57C VAL* 3.5 21.4 + - + +
58C VAL* 1.3 77.4 - - - +
60C VAL* 1.3 64.2 + - - +
61C ARG* 3.9 5.0 + - + +
88C GLU 4.2 0.3 - - - +
89C TRP* 3.6 18.0 - - - +
90C SER 4.6 2.1 + - - -
186C ASP* 3.3 12.8 - - + +
188C GLU* 4.1 36.6 - - + +
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Residues in contact with VAL 60 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58C VAL* 4.1 17.0 - - + -
59C ILE* 1.3 77.5 - - - +
61C ARG* 1.3 73.1 + - - +
62C PHE* 3.4 3.9 + - + +
87C GLN* 4.2 8.5 - - + +
88C GLU 3.8 1.6 - - - -
89C TRP* 3.6 22.4 - - + -
115C TRP* 4.7 2.5 - - + -
117C PRO* 3.6 35.9 - - + -
119C ILE* 5.4 6.5 - - + -
185C ILE* 4.2 20.6 - - + -
186C ASP 2.9 6.7 + - - +
187C LEU* 3.5 9.4 - - + +
188C GLU 3.3 19.6 + - - -
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Residues in contact with ARG 61 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59C ILE* 3.9 5.1 + - + +
60C VAL* 1.3 72.4 - - - +
62C PHE* 1.3 58.0 + - - +
87C GLN* 3.2 6.1 - - - -
88C GLU* 2.7 64.9 + - + +
188C GLU* 2.1 47.3 + - + +
189C GLN 4.5 3.6 + - - -
190C MET* 2.9 44.7 - - + +
191C GLU* 4.7 4.6 - - - +
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Residues in contact with PHE 62 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60C VAL* 3.4 4.9 + - + +
61C ARG* 1.3 75.1 - - - +
63C GLY* 1.3 75.1 + - - +
64C LEU* 5.0 2.2 - - + -
85C LEU* 3.7 38.4 - - + -
86C LYS 3.3 9.6 - - - -
87C GLN* 3.8 13.0 - - + -
119C ILE* 4.3 7.4 - - + -
175C PHE* 3.6 35.2 - + + -
187C LEU* 3.8 35.2 - - + -
188C GLU 3.1 10.6 + - - +
189C GLN* 3.4 10.1 - - - +
190C MET* 2.7 31.7 + - - +
229C VAL* 4.2 16.6 - - + -
231C TYR* 4.2 12.1 + + - -
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Residues in contact with GLY 63 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62C PHE* 1.3 84.7 - - - +
64C LEU* 1.3 60.4 + - - -
85C LEU 3.9 0.2 - - - -
86C LYS* 2.9 54.5 + - - +
190C MET* 3.6 9.4 - - - -
192C GLN* 5.8 0.4 - - - -
231C TYR* 3.3 9.9 - - - -
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Residues in contact with LEU 64 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62C PHE* 5.2 4.5 - - + -
63C GLY* 1.3 73.4 - - - -
65C SER* 1.3 99.3 + - - +
66C ILE* 4.0 6.5 - - + +
83C VAL* 3.8 20.2 - - + -
84C TRP 4.1 3.1 - - - +
85C LEU* 5.2 2.5 - - + +
86C LYS* 4.4 2.6 + - - -
173C MET* 4.3 6.3 - - - -
175C PHE* 3.7 29.2 - - + -
192C GLN* 5.5 0.4 - - - +
196C LEU* 3.0 28.4 - - + +
231C TYR* 2.8 55.8 + - + -
233C PHE* 3.9 16.2 - - + -
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Residues in contact with SER 65 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64C LEU* 1.3 85.5 + - - +
66C ILE* 1.3 59.9 + - - +
67C ALA 3.9 0.2 - - - -
83C VAL* 3.3 1.0 - - - -
84C TRP* 2.8 47.2 + - - -
86C LYS* 3.2 18.6 + - - +
195C ASP 3.8 5.2 + - - -
196C LEU* 4.0 3.4 - - - +
199C TYR* 2.7 44.1 + - - -
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Residues in contact with ILE 66 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64C LEU* 4.2 6.3 - - + -
65C SER* 1.3 73.7 - - - +
67C ALA* 1.3 59.3 + - - +
68C GLN 4.0 15.9 - - - +
69C LEU* 5.3 1.1 - - + +
79C MET* 5.8 0.7 - - - -
81C THR* 3.9 26.5 - - + -
82C ASN 4.2 3.1 - - - +
83C VAL* 4.6 4.5 - - + +
196C LEU* 2.8 42.8 + - + +
197C LYS* 4.6 1.3 - - + -
199C TYR* 4.1 2.0 - - - -
200C TRP* 3.2 35.0 + - + +
207C ILE* 3.9 19.1 - - + -
233C PHE* 3.7 31.6 - - + -
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Residues in contact with ALA 67 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122B TYR 5.3 3.1 - - - +
65C SER 3.8 2.2 + - - -
66C ILE* 1.3 74.8 - - - +
68C GLN* 1.3 71.3 + - + +
82C ASN* 3.0 20.7 + - - +
84C TRP* 3.6 40.6 - - + +
199C TYR* 3.1 26.2 - - - +
200C TRP* 4.1 1.1 - - - -
201C GLU* 3.4 12.3 + - - +
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Residues in contact with GLN 68 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123B ASN* 3.0 37.3 + - - +
124B ASN 4.7 1.8 + - - -
156B SER 3.4 22.3 + - - +
157B CYS 5.4 2.2 + - - -
172B LYS* 4.0 0.5 + - - -
66C ILE* 3.6 10.9 - - - +
67C ALA* 1.3 86.7 - - + +
69C LEU* 1.3 64.3 + - - +
70C ILE* 3.6 13.6 - - + +
81C THR* 3.7 2.4 - - - -
82C ASN* 2.9 40.3 + - + +
200C TRP* 4.8 3.6 - - - -
201C GLU* 3.2 34.5 - - + +
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Residues in contact with LEU 69 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66C ILE* 5.4 0.7 - - + -
68C GLN* 1.3 74.6 + - - +
70C ILE* 1.3 64.7 + - - +
71C ASP* 3.7 28.0 - - - +
72C VAL* 4.4 9.9 - - + +
79C MET* 4.8 13.2 - - + -
80C THR 3.9 6.7 - - - +
81C THR* 4.8 4.3 - - + +
200C TRP* 4.7 7.8 - - + +
201C GLU 5.6 1.2 + - - -
203C GLY* 5.6 3.8 - - - -
204C GLU* 4.2 13.9 - - - +
205C TRP* 4.0 22.7 - - + +
206C ALA 4.2 0.7 - - - +
207C ILE* 3.9 33.9 - - + -
235C ILE* 4.1 22.9 - - + -
237C ARG* 5.1 2.9 - - - +
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Residues in contact with ILE 70 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77B GLN* 3.7 26.6 - - + +
124B ASN 5.4 0.2 - - - +
125B ALA* 3.3 46.4 - - + +
126B ASP* 4.5 2.0 - - - +
156B SER* 5.5 5.2 - - - +
159B ILE* 5.5 1.2 - - - +
68C GLN* 4.2 14.6 - - + +
69C LEU* 1.3 74.5 - - - +
71C ASP* 1.3 62.0 + - + +
80C THR* 2.9 35.1 + - + -
81C THR 3.7 7.4 - - - -
82C ASN* 3.7 19.1 - - + +
152C ILE* 3.4 19.1 - - + -
204C GLU* 5.3 4.0 - - - +
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Residues in contact with ASP 71 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76B ASN* 2.8 26.5 + - - -
77B GLN* 3.4 36.1 + - + +
126B ASP* 5.4 0.3 - - - +
69C LEU* 3.5 11.4 - - - +
70C ILE* 1.3 83.9 - - + +
72C VAL* 1.3 77.2 + - - +
73C ASP* 4.2 12.0 + - - +
78C MET 4.4 0.2 - - - +
79C MET* 3.8 2.9 - - - -
80C THR* 3.0 40.9 + - - +
205C TRP* 6.5 0.7 - - - -
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Residues in contact with VAL 72 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76B ASN* 4.3 5.5 + - - -
69C LEU* 4.7 9.0 - - + -
71C ASP* 1.3 82.7 + - - +
73C ASP* 1.3 68.6 + - - +
74C GLU* 4.2 3.2 + - + +
78C MET 4.2 5.8 - - - +
79C MET* 5.0 3.8 - - + +
169C GLN* 4.3 15.5 - - - +
205C TRP* 4.4 20.1 - - + -
235C ILE* 5.0 4.7 - - + -
237C ARG* 2.9 52.0 + - - +
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Residues in contact with ASP 73 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76B ASN* 5.0 5.6 - - - +
71C ASP* 4.0 15.7 + - - +
72C VAL* 1.3 77.4 - - - +
74C GLU* 1.3 71.0 + - - +
75C LYS* 3.4 21.7 + - - +
76C ASN* 4.2 10.9 + - + +
77C GLN* 3.5 1.7 + - - -
78C MET* 3.3 35.7 + - + +
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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