Contacts of the strand formed by residues 86 - 97 (chain 0) in PDB entry 4UOW
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 GLY 86 (chain 0).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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40 PRO* 4.5 2.5 - - - -
50 PRO* 3.5 10.0 - - - +
820 GLY* 3.5 0.2 - - - -
830 ASN* 2.9 33.5 + - - +
840 GLU 3.6 1.0 + - - -
850 PHE* 1.3 79.5 - - - +
870 SER* 1.3 62.7 + - - -
682 ASP* 5.2 3.1 - - - -
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Residues in contact with SER 87 (chain 0).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40 PRO* 5.4 0.6 - - - +
50 PRO* 3.8 10.8 - - - +
810 LEU 3.3 15.7 - - - -
820 GLY* 4.2 3.6 - - - -
860 GLY* 1.3 74.3 - - - -
880 ASP* 1.3 63.4 + - - +
682 ASP* 5.5 3.6 + - - +
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Residues in contact with ASP 88 (chain 0).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50 PRO* 3.6 17.4 - - - +
60 LYS* 3.5 23.2 + - - +
70 ILE* 2.7 39.4 + - + +
800 SER* 3.4 2.9 - - - -
810 LEU* 2.9 36.7 + - + +
870 SER* 1.3 75.7 - - - +
890 SER* 1.3 71.9 + - - +
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Residues in contact with SER 89 (chain 0).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70 ILE* 3.7 2.4 - - - +
780 THR* 4.2 12.9 - - - +
790 LEU 3.3 9.6 - - - -
800 SER* 4.2 11.0 - - - -
880 ASP* 1.3 85.5 + - - +
900 ALA* 1.3 62.0 + - - +
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Residues in contact with ALA 90 (chain 0).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70 ILE* 3.8 26.7 - - + -
100 LEU* 3.8 20.5 - - + +
780 THR* 3.3 3.8 - - - +
790 LEU* 2.9 32.2 + - + +
890 SER* 1.3 76.2 - - - +
910 THR* 1.3 65.9 + - - +
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Residues in contact with THR 91 (chain 0).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100 LEU* 3.6 5.3 - - - +
110 PRO 3.5 10.2 - - - +
120 SER* 3.8 9.4 - - - +
760 LEU* 3.8 32.5 - - + +
770 TYR 3.2 4.0 - - - +
780 THR* 3.4 30.7 - - + +
900 ALA* 1.3 78.8 - - - +
920 VAL* 1.3 59.9 + - - +
930 ASN 4.2 0.2 - - - -
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Residues in contact with VAL 92 (chain 0).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100 LEU* 3.8 10.5 - - + -
110 PRO* 3.3 24.0 - - + +
120 SER 3.4 3.6 - - - +
140 ILE* 3.7 36.3 - - + -
240 VAL* 4.9 8.1 - - + -
380 TRP* 3.9 20.6 - - + -
760 LEU* 4.5 2.0 - - - -
770 TYR* 2.8 52.8 + - + +
910 THR* 1.3 71.2 - - - +
930 ASN* 1.3 62.6 + - - +
940 ILE* 3.4 12.4 + - + -
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Residues in contact with ASN 93 (chain 0).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120 SER 2.8 13.6 + - - +
130 ASP* 3.3 21.9 + - - +
140 ILE 2.9 28.2 + - - +
750 GLY* 3.5 15.9 - - - +
760 LEU* 3.8 24.5 - - + +
910 THR 4.2 0.2 - - - -
920 VAL* 1.3 70.4 - - - +
940 ILE* 1.3 60.9 + - - +
950 HIS* 3.2 26.8 + - - -
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Residues in contact with ILE 94 (chain 0).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140 ILE* 3.5 23.6 - - + +
160 ILE* 4.6 1.8 - - + -
220 LEU* 3.6 34.8 - - + -
240 VAL* 4.7 1.8 - - + -
640 LEU* 4.1 9.9 - - + -
660 ILE* 4.0 11.9 - - + -
730 ASP* 4.9 1.3 - - + +
740 GLY* 3.4 3.8 - - - -
750 GLY* 2.9 37.6 + - - +
770 TYR* 3.5 38.8 - - + -
920 VAL* 4.1 10.8 - - + +
930 ASN* 1.3 74.3 - - - +
950 HIS* 1.3 65.1 + - - +
960 ILE* 3.9 19.7 - - + -
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Residues in contact with HIS 95 (chain 0).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130 ASP* 2.9 30.0 + - + -
140 ILE 2.8 22.0 + - - -
150 SER* 3.3 21.2 - - - +
160 ILE* 3.0 27.0 + - - +
740 GLY* 5.0 0.2 - - - -
930 ASN* 3.2 36.9 + - - -
940 ILE* 1.3 73.6 + - - +
960 ILE* 1.3 68.9 + - - +
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Residues in contact with ILE 96 (chain 0).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160 ILE* 3.4 7.9 - - + +
180 GLU* 3.7 29.2 - - + +
690 VAL* 3.4 34.1 - - + -
700 GLN 3.9 2.9 - - - +
710 LYS* 3.0 48.8 + - + +
730 ASP* 4.3 3.6 - - + -
740 GLY* 3.5 33.3 - - - +
940 ILE* 3.9 18.2 - - + -
950 HIS* 1.3 85.1 - - - +
970 ARG* 1.3 63.5 + - - +
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Residues in contact with ARG 97 (chain 0).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150 SER* 3.2 45.4 + - - -
160 ILE 3.0 14.6 + - - +
170 ASP* 2.8 40.1 + - - +
180 GLU* 3.0 32.5 + - - +
710 LYS* 4.7 4.3 - - - +
950 HIS* 6.4 0.2 - - + -
960 ILE* 1.3 73.8 - - - +
980 SER* 1.4 63.3 + - - +
831 ARG* 5.3 10.5 - - - +
851 ARG* 3.9 10.5 - - - +
901 GLU* 4.0 7.1 + - - -
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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