Contacts of the strand formed by residues 78 - 90 (chain D) 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 MET 78 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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71D ASP 4.1 0.5 - - - +
72D VAL* 3.3 3.0 - - - -
73D ASP* 2.5 42.4 + - + +
76D ASN* 3.2 26.2 - - + +
77D GLN* 1.3 79.5 - - - +
79D MET* 1.3 62.1 + - - +
80D THR* 5.7 1.6 - - - +
126D ASP* 3.6 25.8 - - - +
154D LYS* 5.0 9.9 - - + -
155D SER 3.1 16.8 - - - +
156D SER* 3.9 6.1 - - - -
157D CYS* 3.9 5.4 - - - -
70E ILE* 4.1 15.7 - - + +
204E GLU* 3.9 19.7 - - - +
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Residues in contact with MET 79 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69D LEU* 3.6 30.1 - - + -
71D ASP 3.4 4.0 - - - +
72D VAL* 4.0 6.7 - - + +
78D MET* 1.3 74.8 - - - +
80D THR* 1.3 63.1 + - - +
81D THR* 3.8 16.9 + - + -
153D TYR 3.7 0.5 - - - +
154D LYS* 3.6 0.6 - - - -
155D SER* 2.7 68.7 + - - +
157D CYS* 3.6 9.8 - - - -
171D CYS* 3.2 44.9 - - + +
173D MET* 4.4 9.6 - - + -
233D PHE* 5.2 12.6 - - + -
235D ILE* 5.2 3.6 - - + -
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Residues in contact with THR 80 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126C ASP* 5.3 1.8 - - - +
69D LEU* 3.8 1.6 - - - +
70D ILE* 2.8 58.5 + - + -
71D ASP* 2.6 25.3 + - - +
78D MET* 4.3 1.9 + - - +
79D MET* 1.3 73.3 - - - +
81D THR* 1.3 68.4 + - - +
152D ILE* 4.4 8.5 - - + -
153D TYR 3.3 8.1 - - - +
154D LYS* 3.4 26.4 - - + +
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Residues in contact with THR 81 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66D ILE* 3.8 19.7 - - + -
68D GLN 3.5 5.4 - - - +
69D LEU* 3.8 22.2 - - + -
70D ILE* 4.1 3.1 - - - -
79D MET* 3.8 16.3 + - - +
80D THR* 1.3 78.8 - - - +
82D ASN* 1.3 59.9 + - - +
83D VAL* 3.8 14.2 - - - +
152D ILE* 3.3 7.3 - - - +
153D TYR* 2.8 33.8 + - - +
155D SER* 5.4 0.2 - - - -
173D MET* 3.4 31.4 - - - +
233D PHE* 5.8 1.6 - - + -
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Residues in contact with ASN 82 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122C TYR 4.2 6.7 + - - -
123C ASN 4.2 16.0 + - - -
124C ASN* 4.6 4.2 + - - +
129C PHE* 3.2 33.3 - - - -
66D ILE* 4.2 0.7 - - - +
67D ALA* 3.2 41.9 + - - +
68D GLN* 3.0 21.9 + - + +
70D ILE* 4.1 12.2 - - + +
81D THR* 1.3 71.1 - - - +
83D VAL* 1.3 66.1 + - - +
84D TRP* 4.8 3.8 - - - +
150D PRO* 4.9 0.5 - - - +
151D ALA 3.3 8.8 - - - +
152D ILE* 3.4 13.3 - - + +
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Residues in contact with VAL 83 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64D LEU* 3.9 19.7 - - + -
65D SER 3.3 12.6 - - - +
66D ILE* 4.8 5.8 - - + -
81D THR* 3.8 25.8 - - - +
82D ASN* 1.3 80.1 - - - +
84D TRP* 1.3 74.2 + - - +
85D LEU* 4.5 7.6 - - + +
149D PRO 4.0 0.2 - - - +
150D PRO* 3.4 3.8 - - - +
151D ALA* 2.7 46.4 + - + +
153D TYR* 3.9 28.0 - - + -
173D MET* 4.8 6.5 - - - -
175D PHE* 5.1 0.9 - - + -
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Residues in contact with TRP 84 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122C TYR* 4.4 13.7 + + - -
178C TRP* 3.3 36.3 - + + -
219C TYR* 4.1 16.4 - + - -
221C CYS* 4.5 11.7 - - + -
300C EPJ 3.7 25.6 - - + -
63D GLY 3.7 0.7 - - - +
64D LEU* 3.8 2.1 - - - -
65D SER* 2.9 52.2 + - - +
67D ALA* 3.7 27.8 - - + +
82D ASN* 4.8 4.9 - - - +
83D VAL* 1.3 87.0 - - - +
85D LEU* 1.3 60.5 + - - +
86D LYS 3.6 2.1 + - - -
148D VAL* 4.0 17.0 - - + -
149D PRO 3.6 4.9 - - - +
150D PRO* 4.5 2.9 - - + +
199D TYR* 3.6 40.4 - + + -
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Residues in contact with LEU 85 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62D PHE* 3.5 31.0 - - + -
63D GLY 4.9 0.9 - - - +
64D LEU* 5.0 4.0 - - + -
83D VAL* 4.6 10.5 - - + -
84D TRP* 1.3 72.3 - - - +
86D LYS* 1.3 65.3 + - - +
87D GLN* 3.3 11.8 + - - +
119D ILE* 5.2 10.3 - - + +
131D VAL* 3.9 22.9 - - + -
147D TRP 3.3 3.8 - - - +
148D VAL* 3.4 3.2 - - - -
149D PRO* 3.0 41.3 + - + +
151D ALA* 5.1 1.3 - - + -
153D TYR* 3.5 23.6 - - + +
175D PHE* 3.8 25.4 - - + -
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Residues in contact with LYS 86 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221C CYS* 4.1 18.8 - - + +
61D ARG 4.0 1.1 - - - -
62D PHE* 3.2 13.0 - - - -
63D GLY* 2.6 63.4 + - - +
64D LEU 3.8 5.7 + - - +
65D SER* 3.2 26.2 + - - +
84D TRP 4.5 1.8 - - - +
85D LEU* 1.3 70.1 - - - +
87D GLN* 1.3 60.3 + - - +
147D TRP 4.0 2.2 - - - -
148D VAL* 4.6 17.7 - - + -
190D MET* 3.4 29.5 - - + +
191D GLU 4.7 1.0 + - - -
194D VAL* 3.6 40.0 + - - +
195D ASP 4.9 1.2 + - - -
196D LEU* 5.2 0.4 - - - +
199D TYR* 4.8 3.2 + - - -
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Residues in contact with GLN 87 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60D VAL* 4.5 4.5 - - + -
61D ARG 3.3 3.4 - - - -
62D PHE* 4.5 10.8 - - + -
85D LEU* 3.6 13.0 - - - +
86D LYS* 1.3 80.1 - - - +
88D GLU* 1.3 64.4 + - - +
89D TRP* 3.7 17.3 - - + -
117D PRO* 3.9 24.0 + - - +
119D ILE* 4.0 23.7 - - + +
131D VAL* 4.9 0.2 - - - +
146D HIS* 3.7 4.7 - - - +
147D TRP* 2.8 69.4 + - - +
148D VAL* 4.9 1.4 - - - +
149D PRO* 3.4 17.3 - - - +
190D MET* 5.4 0.9 - - - -
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Residues in contact with GLU 88 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59D ILE 3.8 0.3 - - - +
60D VAL* 3.2 4.9 - - - +
61D ARG* 2.5 88.7 + - + +
87D GLN* 1.3 77.9 - - - +
89D TRP* 1.3 66.6 + - - +
144D THR* 4.3 10.2 - - + +
145D VAL 3.4 12.6 - - - +
146D HIS* 3.6 29.5 + - + +
190D MET* 4.9 4.5 - - - +
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Residues in contact with TRP 89 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52D PRO* 4.5 1.8 - - + -
58D VAL* 4.3 5.8 - - + -
59D ILE 3.4 18.2 - - - +
60D VAL* 4.1 15.3 - - + -
87D GLN* 3.7 26.0 - - + -
88D GLU* 1.3 87.4 - - - +
90D SER* 1.3 76.4 + - - +
91D ASP* 4.3 4.0 - - - +
115D TRP* 3.1 54.1 + + - -
116D ILE* 3.8 10.1 - - + -
117D PRO* 3.7 20.4 - - + -
144D THR* 3.7 4.9 - - - +
145D VAL* 2.9 65.9 + - + +
147D TRP* 3.7 20.6 - + + -
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Residues in contact with SER 90 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52D PRO* 3.6 13.7 - - - +
53D ASN* 5.8 0.3 - - - +
58D VAL* 4.6 7.6 - - - +
59D ILE 4.4 3.4 + - - -
89D TRP* 1.3 83.5 - - - +
91D ASP* 1.3 60.6 + - - +
92D TYR 3.9 0.6 + - - -
142D THR 5.6 0.3 + - - -
143D GLY 3.4 7.3 - - - -
144D THR* 3.8 16.1 + - - +
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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