Contacts of the strand formed by residues 58 - 73 (chain E) 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 E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51E VAL* 3.2 37.5 - - + -
52E PRO* 4.1 10.3 - - + +
53E ASN* 4.3 7.4 - - - +
57E VAL* 1.3 70.5 - - - +
59E ILE* 1.3 63.4 + - - +
60E VAL* 4.7 3.6 - - + -
89E TRP* 4.0 29.2 - - + -
90E SER 4.8 6.7 - - - +
115E TRP* 4.3 15.7 - - + -
184E LYS 3.1 11.5 + - - +
185E ILE* 3.3 12.1 - - + +
186E ASP 2.9 25.8 + - - +
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Residues in contact with ILE 59 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57E VAL* 3.7 16.7 + - + +
58E VAL* 1.3 74.7 - - - +
60E VAL* 1.3 64.8 + - - +
61E ARG* 3.9 2.5 + - + +
88E GLU 3.6 7.6 - - - +
89E TRP* 3.7 11.6 - - - +
90E SER 4.8 1.2 + - - -
186E ASP* 3.2 37.9 - - + +
188E GLU* 4.1 31.0 - - + +
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Residues in contact with VAL 60 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58E VAL* 4.7 4.9 - - + -
59E ILE* 1.3 77.7 - - - +
61E ARG* 1.3 76.0 + - - +
62E PHE* 3.2 9.4 + - + +
87E GLN* 4.2 16.2 - - + +
88E GLU 3.2 16.8 - - - +
89E TRP* 4.2 13.9 - - + -
115E TRP* 5.4 0.2 - - + -
117E PRO* 4.4 17.7 - - + -
119E ILE* 5.1 1.6 - - + -
185E ILE* 4.4 16.8 - - + -
186E ASP 2.8 15.9 + - - +
187E LEU* 3.4 15.0 - - + -
188E GLU 2.8 26.0 + - - +
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Residues in contact with ARG 61 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59E ILE* 3.9 3.8 + - + -
60E VAL* 1.3 72.5 - - - +
62E PHE* 1.3 59.9 + - - +
86E LYS* 3.1 12.7 - - - +
87E GLN* 3.6 2.6 - - - -
88E GLU* 2.9 73.8 + - + +
146E HIS* 4.8 0.6 + - - -
188E GLU* 3.0 37.7 - - + +
189E GLN 5.5 0.2 - - - -
190E MET* 3.5 35.5 - - + +
191E GLU* 4.2 6.5 - - - +
193E THR* 3.5 26.7 + - - +
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Residues in contact with PHE 62 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60E VAL* 3.8 9.6 - - + +
61E ARG* 1.3 75.7 - - - +
63E GLY* 1.3 60.5 + - - +
85E LEU* 3.3 36.8 - - + -
86E LYS 3.5 10.5 - - - -
87E GLN* 3.7 21.3 - - + -
119E ILE* 3.9 17.0 - - + -
175E PHE* 3.7 32.5 - + + -
187E LEU* 3.7 25.8 - - + -
188E GLU 2.9 9.6 + - - +
189E GLN* 3.8 5.7 - - - +
190E MET* 3.1 22.7 + - - +
192E GLN* 5.3 0.7 + - - -
229E VAL* 4.2 25.8 - - + -
231E TYR* 3.7 14.1 + + - -
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Residues in contact with GLY 63 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62E PHE* 1.3 79.9 - - - +
64E LEU* 1.3 58.7 + - - -
84E TRP 3.6 0.3 - - - +
85E LEU* 3.7 1.5 - - - -
86E LYS* 2.6 48.1 + - - +
190E MET* 3.1 6.7 - - - -
192E GLN* 4.8 2.9 - - - -
194E VAL* 3.2 22.3 - - - +
231E TYR* 3.6 6.5 - - - -
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Residues in contact with LEU 64 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63E GLY* 1.3 73.2 - - - -
65E SER* 1.3 59.5 + - - +
66E ILE* 3.7 26.5 - - + -
83E VAL* 3.9 18.2 - - + -
84E TRP 3.0 22.7 - - - +
85E LEU* 3.9 20.4 - - + -
173E MET* 4.8 3.1 - - - -
175E PHE* 4.5 9.9 - - + -
192E GLN* 4.6 2.4 + - - -
194E VAL* 3.4 9.8 - - - +
196E LEU* 3.2 27.8 - - + +
231E TYR* 3.4 49.4 + - + -
233E PHE* 4.5 9.4 - - + -
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Residues in contact with SER 65 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221D CYS* 4.5 1.4 - - - +
63E GLY 4.1 0.4 + - - -
64E LEU* 1.3 71.7 - - - +
66E ILE* 1.3 62.9 + - - +
67E ALA 4.0 0.4 + - - -
83E VAL* 3.4 6.1 - - - +
84E TRP* 2.7 68.3 + - - +
194E VAL* 3.0 23.7 - - - +
195E ASP 3.0 20.7 + - - -
196E LEU 3.7 0.2 - - - -
199E TYR 5.8 1.3 - - - -
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Residues in contact with ILE 66 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64E LEU* 3.7 30.5 - - + -
65E SER* 1.3 76.1 - - - +
67E ALA* 1.3 56.1 + - - +
68E GLN 3.8 17.7 - - - +
81E THR* 5.3 3.4 - - + -
82E ASN 4.0 2.7 - - - +
83E VAL* 3.8 17.0 - - + -
84E TRP* 5.7 0.4 - - - -
196E LEU* 2.9 26.2 + - + +
197E LYS* 4.6 9.9 - - + -
199E TYR 2.7 23.7 + - - +
200E TRP* 3.1 36.4 - - + +
207E ILE* 5.4 4.7 - - + -
233E PHE* 3.9 26.9 - - + -
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Residues in contact with ALA 67 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122D TYR 4.6 4.7 - - - +
65E SER 4.0 1.6 + - - -
66E ILE* 1.3 75.1 - - - +
68E GLN* 1.3 68.6 + - + +
82E ASN* 2.9 35.2 + - - +
84E TRP* 3.6 28.2 - - + +
199E TYR 3.8 7.4 - - - -
200E TRP* 3.9 1.5 - - - +
201E GLU* 3.3 25.5 + - - +
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Residues in contact with GLN 68 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123D ASN* 3.5 10.5 + - - +
124D ASN* 3.1 19.8 - - + +
156D SER* 2.8 29.9 + - - -
66E ILE* 3.5 10.9 - - - +
67E ALA* 1.3 87.5 + - + +
69E LEU* 1.3 59.1 + - - +
70E ILE* 2.7 37.3 - - + +
81E THR* 3.5 10.6 - - - +
82E ASN* 3.1 38.8 + - + +
200E TRP* 4.3 2.7 - - - +
201E GLU* 4.2 26.3 + - - +
204E GLU* 3.9 7.2 - - - +
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Residues in contact with LEU 69 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68E GLN* 1.3 69.8 - - - +
70E ILE* 1.3 60.0 + - - +
71E ASP 4.7 7.2 - - - +
72E VAL* 5.5 9.4 - - + -
79E MET* 4.2 14.4 - - + -
80E THR 3.8 12.3 - - - +
81E THR* 3.8 15.0 - - + -
200E TRP* 4.0 19.5 - - + +
201E GLU 4.8 1.0 + - - -
204E GLU* 2.8 38.2 + - + +
205E TRP* 4.5 9.4 - - + +
206E ALA 3.8 20.0 - - - +
207E ILE* 3.3 36.1 - - + +
235E ILE* 4.4 12.3 - - + -
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Residues in contact with ILE 70 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77D GLN* 3.6 7.4 + - - -
78D MET* 4.1 11.9 - - + +
124D ASN* 3.6 14.4 - - + -
126D ASP* 4.0 27.8 - - + +
156D SER* 5.2 0.4 - - - -
68E GLN* 2.7 47.3 - - + +
69E LEU* 1.3 72.6 - - - +
71E ASP* 1.3 63.7 + - + +
80E THR* 2.6 39.5 + - + +
81E THR 4.5 0.4 - - - -
82E ASN* 4.4 10.5 - - + +
152E ILE* 5.0 1.6 - - + -
204E GLU* 2.9 24.2 - - - +
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Residues in contact with ASP 71 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76D ASN* 3.5 25.0 + - - +
77D GLN* 4.9 5.4 + - - +
69E LEU* 3.6 3.2 - - - +
70E ILE* 1.3 88.6 - - + +
72E VAL* 1.3 66.5 + - - +
73E ASP* 3.4 28.7 - - - +
78E MET* 4.4 0.7 - - - +
79E MET* 3.6 1.4 - - - +
80E THR* 2.7 46.1 + - + +
204E GLU* 4.9 3.4 - - - -
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Residues in contact with VAL 72 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69E LEU* 5.5 9.2 - - + -
71E ASP* 1.3 79.5 + - - +
73E ASP* 1.3 62.6 + - - +
74E GLU 4.2 0.2 + - - -
78E MET 3.8 11.4 - - - +
79E MET* 4.7 10.8 - - + -
157E CYS* 6.5 0.7 - - - -
159E ILE* 4.5 16.8 - - + -
160E ASP* 5.6 2.2 - - - +
204E GLU* 6.4 1.3 - - + -
205E TRP* 3.2 60.1 - - + -
235E ILE* 4.9 11.2 - - + -
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Residues in contact with ASP 73 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71E ASP* 3.4 21.3 + - - +
72E VAL* 1.3 76.5 - - - +
74E GLU* 1.3 57.1 + - - +
75E LYS* 3.6 4.6 + - + +
76E ASN* 2.5 49.6 + - - +
77E GLN 3.2 14.7 + - - -
78E MET* 3.3 33.9 + - - +
159E ILE* 3.7 6.1 - - - +
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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
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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