Contacts of the strand formed by residues 69 - 83 (chain 1) in PDB entry 5NET
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 ALA 69 (chain 1).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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651 LEU 4.6 0.6 + - - +
661 LEU* 3.1 11.0 + - - +
671 ARG 3.9 3.3 - - - +
681 THR* 1.3 81.0 - - - +
701 THR* 1.3 56.8 + - - +
711 TYR 3.8 9.4 - - - +
721 TYR* 4.7 4.3 - - + -
1281 THR* 2.7 33.3 + - + +
1851 THR* 3.7 36.8 - - + -
1861 TYR 3.8 8.7 - - - +
1871 CYS 4.2 0.4 - - - -
1881 PRO* 4.6 1.8 - - - -
1891 ARG* 4.0 2.6 - - - +
413 PHE* 4.5 3.6 - - + -
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Residues in contact with THR 70 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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691 ALA* 1.3 73.3 - - - +
711 TYR* 1.3 81.6 + - + +
1271 ALA* 3.3 7.6 - - + +
1281 THR* 3.0 29.2 + - - +
1291 VAL* 5.6 2.0 - - + +
1861 TYR 3.1 1.0 + - - -
1871 CYS* 2.4 42.4 + - - +
1891 ARG* 3.2 34.8 - - - +
1272 PRO* 4.4 9.0 - - + +
1282 GLU* 4.3 13.2 - - + -
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Residues in contact with TYR 71 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
691 ALA* 3.8 2.5 - - - +
701 THR* 1.3 100.2 - - + +
721 TYR* 1.3 60.9 + - - +
1251 VAL* 3.6 16.8 - - + -
1261 LEU 3.3 14.4 - - - -
1271 ALA* 3.7 10.5 - - + -
1851 THR* 3.5 1.9 - - - -
1861 TYR* 2.8 42.6 + - + +
1871 CYS* 4.1 16.8 - - - -
1272 PRO* 4.8 2.5 - - + -
1282 GLU* 3.4 27.6 + - + +
1632 VAL* 4.2 18.5 - - + +
1642 GLY* 3.6 29.2 + - - -
1652 VAL* 3.6 33.8 + - + -
1762 PRO* 5.4 0.9 - - - +
373 LEU* 5.5 6.3 - - + -
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Residues in contact with TYR 72 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
521 ASP* 5.0 2.8 + - - -
531 LEU* 3.7 46.3 + - + +
541 MET* 4.8 6.9 - - + +
661 LEU* 3.9 26.5 - - + -
691 ALA* 4.7 2.9 - - + -
711 TYR* 1.3 75.5 - - - +
731 PHE* 1.3 62.2 + - - +
741 ALA 4.5 3.1 - - - -
1251 VAL* 3.4 4.7 - - - +
1261 LEU* 3.1 55.7 + - + +
1271 ALA 3.6 28.0 + - - -
1281 THR* 4.0 21.8 - - + -
1631 PHE* 5.6 2.4 + - - +
1651 TYR* 3.8 14.6 - - - -
1801 MET* 4.5 7.0 - - + -
1841 GLU 3.3 9.9 - - - +
1851 THR* 4.5 8.5 - - + -
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Residues in contact with PHE 73 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
721 TYR* 1.3 73.6 - - - +
741 ALA* 1.3 66.8 + - - +
751 ASP* 4.4 4.3 - - - -
1191 TYR* 3.4 47.6 - + + -
1241 ARG 4.9 0.2 - - - +
1251 VAL* 4.2 6.3 - - + +
1821 ARG* 3.9 27.8 - - - -
1831 ALA* 3.3 1.0 - - - -
1841 GLU* 2.7 50.2 + - + +
1861 TYR* 5.1 1.1 - - + -
313 ASN* 3.8 11.9 - - + -
343 ARG* 3.1 59.0 - - - +
334 SER* 3.9 2.0 - - - -
354 ASP* 3.5 18.2 - - - -
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Residues in contact with ALA 74 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
531 LEU* 5.1 0.2 - - + -
721 TYR* 4.3 3.1 - - + -
731 PHE* 1.3 83.1 - - - +
751 ASP* 1.3 62.6 + - - +
1191 TYR* 4.2 3.3 - - - -
1651 TYR* 2.4 41.4 + - - +
1801 MET* 3.7 44.0 - - + -
1811 LYS 3.6 9.9 - - - +
1821 ARG 4.4 1.8 - - - -
1831 ALA* 3.9 6.1 - - - +
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Residues in contact with ASP 75 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
731 PHE* 4.4 2.0 - - - -
741 ALA* 1.3 72.5 - - - +
761 LEU* 1.3 60.7 + - - +
1171 LEU 4.1 10.1 - - - +
1181 PRO* 4.7 0.2 - - - -
1191 TYR* 3.1 31.0 + - - +
1651 TYR* 4.8 1.3 - - - -
1801 MET* 3.4 3.0 - - - -
1811 LYS* 2.8 51.9 + - + +
1821 ARG* 2.5 39.5 + - - +
324 ASN* 3.6 8.1 + - - +
334 SER* 3.1 21.5 + - - -
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Residues in contact with LEU 76 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
511 LEU* 4.0 17.0 - - + +
531 LEU* 3.7 28.9 - - + -
741 ALA 3.7 1.2 + - - -
751 ASP* 1.3 73.6 - - - +
771 GLU* 1.3 61.1 + - - +
781 VAL* 3.9 22.0 - - + -
1161 ALA* 5.0 0.2 - - - +
1171 LEU* 2.8 37.3 + - + +
1651 TYR* 3.8 47.5 - - + -
1781 TYR* 4.0 19.7 - - + -
1791 ARG 3.3 18.6 - - - +
1801 MET* 4.6 0.4 - - - +
1811 LYS* 5.7 0.4 - - - -
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Residues in contact with GLU 77 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
391 PHE* 4.4 2.9 - - + -
751 ASP 4.1 0.8 + - - -
761 LEU* 1.3 75.7 - - - +
781 VAL* 1.3 65.2 + - - +
1141 ARG* 3.3 15.4 + - - -
1151 LEU 3.5 13.7 - - - +
1161 ALA* 3.6 13.2 - - + +
1171 LEU* 4.2 0.4 - - - +
1771 LEU 4.2 0.2 - - - +
1791 ARG* 3.2 56.5 + - + +
1811 LYS* 2.8 36.0 + - + +
213 THR* 4.2 0.3 - - - -
223 ALA* 2.6 41.2 + - + +
314 GLN* 5.4 0.2 + - - -
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Residues in contact with VAL 78 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
391 PHE* 4.5 2.3 - - - -
511 LEU* 4.3 14.6 - - + -
761 LEU* 3.9 17.9 - - + -
771 GLU* 1.3 79.4 - - - +
791 ALA* 1.3 62.5 + - - +
801 VAL* 4.9 9.2 - - + -
1141 ARG* 3.3 5.4 - - - +
1151 LEU* 3.2 52.0 + - + +
1171 LEU* 4.3 12.3 - - + -
1681 ILE* 5.4 7.0 - - + -
1761 LEU* 5.9 2.5 - - + -
1771 LEU 3.3 8.3 - - - +
1781 TYR* 3.8 28.3 - - + -
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Residues in contact with ALA 79 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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391 PHE* 3.6 26.2 - - + -
781 VAL* 1.3 76.5 - - - +
801 VAL* 1.3 55.9 + - - +
1121 LEU* 4.6 13.9 - - + -
1131 THR 3.9 5.4 - - - -
1141 ARG* 3.7 14.1 - - + -
1751 GLU 3.8 0.2 - - - +
1761 LEU* 3.5 1.2 - - - -
1771 LEU* 2.7 45.2 + - + +
143 LEU* 4.6 8.1 - - + -
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Residues in contact with VAL 80 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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781 VAL* 4.9 6.7 - - + -
791 ALA* 1.3 74.4 - - - +
811 LYS* 1.3 67.6 + - - +
821 HIS* 3.6 6.3 + - + +
861 LEU* 3.7 42.2 - - + -
1121 LEU* 4.1 3.3 - - - +
1131 THR* 3.1 47.0 + - - +
1151 LEU* 4.9 4.5 - - + -
1681 ILE* 5.5 1.6 - - + -
1731 VAL* 3.9 16.2 - - + -
1751 GLU 3.6 3.8 - - - +
1761 LEU* 3.8 24.2 - - + +
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Residues in contact with LYS 81 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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801 VAL* 1.3 71.2 - - - +
821 HIS* 1.3 62.3 + - - +
1111 PRO* 3.5 39.9 + - + +
1121 LEU* 4.0 19.2 - - + +
1731 VAL* 4.1 0.3 - - - -
1741 THR* 2.4 47.8 + - + +
1751 GLU* 2.9 22.7 + - + +
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Residues in contact with HIS 82 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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801 VAL* 3.6 21.1 + - + +
811 LYS* 1.3 76.9 - - - +
831 GLU* 1.3 75.3 + - - +
841 GLY 3.5 27.8 + - - -
851 ASN 4.4 0.2 - - - -
861 LEU* 4.0 20.9 - - + +
1061 ALA 4.0 12.2 + - - -
1081 HIS* 3.1 34.9 + - - -
1111 PRO 4.5 3.1 + - - +
1121 LEU* 5.6 1.1 - - - -
1131 THR* 3.2 36.0 + - + -
1701 ALA* 4.3 3.8 - - + -
1721 ARG 3.8 12.8 - - - +
1731 VAL* 4.1 13.5 - - + -
1741 THR* 4.4 1.3 - - - +
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Residues in contact with GLU 83 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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821 HIS* 1.3 82.5 - - - +
841 GLY* 1.3 63.1 + - - +
1081 HIS* 4.2 9.0 - - + +
1701 ALA* 4.3 0.3 - - - +
1711 THR* 3.4 27.8 + - + +
1721 ARG* 3.0 50.9 + - + +
1741 THR* 3.7 12.6 - - - +
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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