Contacts of the strand formed by residues 58 - 73 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51A VAL* 3.0 37.7 - - + -
52A PRO* 4.0 9.9 - - + +
53A ASN* 3.3 15.3 - - - +
57A VAL* 1.3 74.4 - - - +
59A ILE* 1.3 65.0 + - - +
60A VAL* 4.2 11.0 - - + -
89A TRP* 4.8 6.1 - - + -
90A SER 5.1 5.4 - - - +
115A TRP* 3.8 25.8 - - + -
184A LYS 3.2 6.7 + - - +
185A ILE* 3.2 10.2 - - + +
186A ASP 2.7 31.4 + - - +
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Residues in contact with ILE 59 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A VAL* 3.1 42.1 + - + +
58A VAL* 1.3 74.8 - - - +
60A VAL* 1.3 64.7 + - - +
61A ARG* 4.1 1.8 + - + +
88A GLU 4.2 0.2 - - - +
89A TRP* 3.8 19.4 - - - +
90A SER 4.6 2.1 + - - -
186A ASP* 3.0 15.7 - - + +
187A LEU 5.1 0.2 - - - -
188A GLU* 4.1 34.3 - - + +
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Residues in contact with VAL 60 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A VAL* 4.2 11.7 - - + -
59A ILE* 1.3 79.5 - - - +
61A ARG* 1.3 72.3 + - - +
62A PHE* 3.4 4.8 + - + -
87A GLN* 4.3 17.0 - - + -
88A GLU 3.7 8.1 - - - +
89A TRP* 4.3 6.5 - - + -
115A TRP* 4.8 0.2 - - + -
117A PRO* 4.1 31.6 - - + -
119A ILE* 6.0 4.7 - - + -
185A ILE* 4.0 23.3 - - + -
186A ASP 2.9 9.3 + - - +
187A LEU* 3.2 11.0 - - + +
188A GLU 2.9 27.1 + - - +
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Residues in contact with ARG 61 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59A ILE* 4.1 2.3 + - + -
60A VAL* 1.3 71.1 - - - +
62A PHE* 1.3 58.4 + - - +
87A GLN* 3.2 8.3 - - - -
88A GLU* 2.6 86.6 + - + +
188A GLU* 2.9 37.3 + - + +
190A MET* 2.9 60.7 + - + +
191A GLU* 4.2 15.4 + - - +
193A THR* 5.6 0.4 + - - -
194A VAL* 4.5 11.5 - - - +
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Residues in contact with PHE 62 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60A VAL* 4.3 10.8 - - + +
61A ARG* 1.3 74.4 - - - +
63A GLY* 1.3 72.2 + - - +
64A LEU* 4.9 0.7 - - + -
85A LEU* 3.3 42.6 - - + -
86A LYS 3.3 9.2 - - - -
87A GLN* 4.1 13.0 - - + -
119A ILE* 5.0 11.9 - - + -
175A PHE* 3.6 34.1 - + + -
187A LEU* 4.7 17.3 - - + -
188A GLU 3.1 10.0 + - - +
189A GLN* 3.6 3.9 - - - +
190A MET* 2.6 31.0 + - - +
229A VAL* 4.1 21.5 - - + -
231A TYR* 4.1 21.2 + + - -
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Residues in contact with GLY 63 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62A PHE* 1.3 81.8 - - - +
64A LEU* 1.3 57.1 + - - -
84A TRP 3.6 0.2 - - - +
85A LEU* 3.6 1.9 - - - -
86A LYS* 2.7 64.3 + - - +
190A MET* 3.4 8.5 - - - +
231A TYR* 3.8 7.0 - - - -
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Residues in contact with LEU 64 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62A PHE* 5.1 0.4 - - + -
63A GLY* 1.3 73.9 - - - -
65A SER* 1.3 67.4 + - - +
66A ILE* 4.3 8.7 - - + -
83A VAL* 3.7 21.3 - - + -
84A TRP 3.7 1.6 - - - +
85A LEU* 3.2 33.4 - - + -
86A LYS* 3.8 4.7 + - - +
173A MET* 4.3 7.6 - - - -
175A PHE* 3.6 29.4 - - + -
194A VAL 4.7 0.2 - - - +
195A ASP 3.8 1.7 - - - +
196A LEU* 3.5 22.9 - - + +
231A TYR* 3.4 40.9 + - + -
233A PHE* 4.0 19.3 - - + -
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Residues in contact with SER 65 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64A LEU* 1.3 74.2 + - - +
66A ILE* 1.3 62.2 + - - +
67A ALA 4.0 0.2 - - - -
83A VAL* 3.2 8.0 - - - +
84A TRP* 2.8 61.4 + - - -
86A LYS* 3.4 22.5 - - - +
195A ASP 3.8 1.7 + - - -
196A LEU 3.7 4.3 - - - -
198A ASP* 3.2 25.1 + - - -
199A TYR* 4.2 3.2 - - - -
221E CYS* 4.7 1.4 - - - +
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Residues in contact with ILE 66 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A LEU* 4.3 9.6 - - + -
65A SER* 1.3 79.8 - - - +
67A ALA* 1.3 62.6 + - - +
68A GLN 3.8 20.9 - - - +
69A LEU* 4.6 2.0 - - + +
81A THR* 5.0 8.7 - - + -
82A ASN 4.0 3.8 - - - +
83A VAL* 4.1 14.1 - - + +
196A LEU* 2.8 23.1 + - + +
197A LYS* 5.2 8.5 - - + -
198A ASP* 4.1 3.6 + - - +
199A TYR* 5.6 0.2 - - - -
200A TRP* 3.3 38.8 + - + +
207A ILE* 5.6 5.8 - - + -
233A PHE* 3.1 46.0 - - + -
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Residues in contact with ALA 67 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65A SER 4.0 2.4 + - - -
66A ILE* 1.3 73.9 - - - +
68A GLN* 1.3 73.8 + - + +
82A ASN* 2.9 24.4 + - - +
83A VAL* 4.3 0.2 - - - +
84A TRP* 3.8 35.4 - - + +
199A TYR* 3.6 11.0 - - + +
200A TRP* 3.3 2.8 - - - +
201A GLU* 3.1 23.0 + - - +
122E TYR 5.2 3.1 - - - +
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Residues in contact with GLN 68 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66A ILE* 3.5 9.2 - - - +
67A ALA* 1.3 92.5 - - + +
69A LEU* 1.3 59.4 + - - +
70A ILE* 3.4 16.4 - - + +
81A THR* 3.6 1.4 - - - -
82A ASN* 2.7 39.4 + - + +
200A TRP* 4.1 5.2 - - - -
201A GLU* 3.2 34.7 - - + +
122E TYR 4.8 0.5 - - - +
123E ASN* 2.9 33.6 - - - +
124E ASN 4.6 0.2 - - - -
156E SER* 2.3 36.3 + - - -
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Residues in contact with LEU 69 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66A ILE* 5.3 1.6 - - + -
68A GLN* 1.3 71.7 + - - +
70A ILE* 1.3 66.7 + - - +
71A ASP* 4.8 3.8 - - - +
72A VAL* 4.6 10.8 - - + +
79A MET* 3.5 42.0 - - + -
80A THR 3.8 2.7 - - - +
81A THR* 3.9 10.1 - - + -
200A TRP* 3.7 23.8 - - + +
201A GLU 4.9 1.2 + - - -
203A GLY* 5.2 5.9 + - - +
204A GLU* 4.1 11.1 - - - +
205A TRP* 3.7 41.1 - - + +
207A ILE* 4.4 19.1 - - + -
235A ILE* 4.5 7.6 - - + -
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Residues in contact with ILE 70 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68A GLN* 3.4 27.4 - - + +
69A LEU* 1.3 74.8 - - - +
71A ASP* 1.3 65.3 + - + +
80A THR* 2.5 36.9 + - + +
81A THR 3.8 1.1 - - - +
82A ASN* 3.4 37.7 - - + +
152A ILE* 4.5 0.7 - - + -
204A GLU* 4.1 4.6 - - - +
76E ASN 4.9 2.0 - - - +
77E GLN* 4.0 19.9 - - - +
78E MET* 4.8 9.9 - - + -
124E ASN* 4.2 21.8 - - + +
126E ASP* 4.4 17.3 - - - +
156E SER* 4.6 9.5 - - - -
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Residues in contact with ASP 71 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69A LEU* 3.6 5.1 - - - -
70A ILE* 1.3 85.7 - - + +
72A VAL* 1.3 59.8 + - - +
73A ASP* 3.2 35.9 + - - +
78A MET 4.5 0.2 - - - +
79A MET 3.6 0.2 - - - -
80A THR* 2.6 40.1 + - - -
204A GLU* 5.5 2.0 - - - -
205A TRP* 6.4 0.4 - - - -
75E LYS 3.4 18.7 - - - +
76E ASN* 3.9 21.3 - - - +
77E GLN* 4.3 8.8 + - + +
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Residues in contact with VAL 72 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69A LEU* 4.6 7.2 - - + -
71A ASP* 1.3 78.6 + - - +
73A ASP* 1.3 72.1 + - - +
74A GLU* 4.2 5.8 + - + +
78A MET 3.1 24.0 - - - +
79A MET* 3.9 16.6 - - + -
157A CYS* 5.4 0.9 - - + -
169A GLN* 3.8 19.7 - - - +
171A CYS* 5.0 1.6 - - - -
205A TRP* 3.7 46.1 + - + +
235A ILE* 3.9 16.8 - - + -
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Residues in contact with ASP 73 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71A ASP* 3.2 29.2 + - - +
72A VAL* 1.3 79.1 - - - +
74A GLU* 1.3 60.7 + - - +
75A LYS* 3.1 22.1 + - - +
76A ASN* 3.3 25.6 - - + +
77A GLN 2.8 17.5 + - - -
78A MET 3.2 15.0 + - - +
75E LYS* 4.0 29.2 - - - +
76E ASN* 5.5 1.6 - - - +
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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