Contacts of the strand formed by residues 78 - 85 (chain 9) 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 78 (chain 9).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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459 LYS* 4.7 1.3 - - - -
469 ASP* 3.7 15.3 - - - -
769 ASP 3.6 2.2 + - - -
779 SER* 1.3 73.5 - - - +
799 GLN* 1.4 60.3 + - - -
809 TYR* 3.3 15.3 - - - -
969 GLY* 4.6 1.6 - - - -
979 LEU 2.9 31.5 + - - -
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Residues in contact with GLN 79 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88 GLU 4.7 1.4 - - - +
98 ALA* 3.7 35.1 - - + +
108 LEU 2.9 31.1 + - - +
118 PRO* 3.9 8.9 - - - +
128 SER* 4.5 7.7 + - - +
449 GLU 3.5 2.4 - - - +
469 ASP* 2.9 42.2 + - - +
479 GLN 4.9 0.2 + - - -
789 GLY* 1.4 69.0 - - - -
809 TYR* 1.3 61.6 + - - +
819 VAL* 3.9 10.6 + - + +
949 ALA* 4.4 4.0 - - + -
959 VAL 3.8 4.3 - - - +
969 GLY* 4.4 3.6 - - - -
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Residues in contact with TYR 80 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169 PRO* 5.7 0.2 - - - +
299 LEU* 3.4 31.0 - - + -
439 TRP* 4.5 6.2 - + + -
449 GLU 3.4 4.5 - - - -
459 LYS* 3.3 39.3 - - + +
509 VAL* 4.7 4.0 - - + -
569 PHE* 3.8 19.3 - + - -
679 LEU* 4.0 16.4 - - + -
699 ILE* 3.8 17.6 - - + +
769 ASP* 2.6 35.7 + - - +
789 GLY 3.3 26.2 - - - -
799 GLN* 1.3 72.6 - - - +
819 VAL* 1.3 60.3 + - - +
829 CYS 4.2 0.3 + - - -
949 ALA* 3.3 2.8 - - - +
959 VAL* 2.8 40.1 + - + +
979 LEU* 3.7 16.6 - - + -
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Residues in contact with VAL 81 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118 PRO* 3.7 40.6 - - + -
429 SER 3.8 0.2 - - - +
439 TRP* 3.4 7.7 - - - -
449 GLU* 2.8 58.3 + - + +
479 GLN* 4.8 8.1 - - - +
799 GLN* 4.3 11.9 - - - +
809 TYR* 1.3 74.7 - - - +
829 CYS* 1.3 70.3 + - - +
839 ARG* 4.1 1.9 + - + +
929 PHE* 4.1 13.9 - - + -
939 ALA 3.7 7.0 - - - +
949 ALA* 3.8 14.8 - - + -
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Residues in contact with CYS 82 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129 PHE* 3.7 23.9 - - + -
169 PRO* 3.9 9.2 - - + -
319 CYS* 3.9 14.4 - - - -
339 ILE* 3.9 3.1 - - - -
419 VAL* 3.5 31.6 - - - -
429 SER 3.6 3.1 - - - -
439 TRP* 3.7 24.2 - - + -
809 TYR 4.2 0.8 + - - -
819 VAL* 1.3 75.3 - - - +
839 ARG* 1.3 58.7 + - - +
929 PHE* 3.5 5.5 - - - -
939 ALA 2.8 34.6 + - - +
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Residues in contact with ARG 83 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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985 GLN* 3.6 24.4 + - - +
995 VAL* 3.4 20.2 + - - +
978 ARG* 5.5 6.3 - - - +
409 GLN* 3.2 19.8 + - - +
419 VAL* 3.4 3.4 - - - -
429 SER* 2.8 65.4 + - - +
449 GLU* 6.2 1.6 - - - -
819 VAL* 5.3 2.5 - - + +
829 CYS* 1.3 74.0 - - - +
849 ALA* 1.3 65.4 - - - +
859 ARG* 4.1 20.4 - - + +
909 GLU* 3.8 9.9 - - - +
919 ALA 3.6 4.0 - - - +
929 PHE* 3.5 38.4 - - + -
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Residues in contact with ALA 84 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109 PRO* 3.6 14.8 - - + +
129 PHE* 4.4 2.9 - - + -
339 ILE* 3.6 34.8 - - + -
399 PRO* 4.0 2.5 - - + -
409 GLN 3.5 5.4 - - - -
419 VAL* 3.9 11.0 - - + -
829 CYS 4.1 0.6 - - - -
839 ARG* 1.3 71.4 - - - +
859 ARG* 1.3 59.7 + - - +
909 GLU* 3.3 4.3 - - - +
919 ALA* 2.8 46.9 + - + +
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Residues in contact with ARG 85 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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965 GLY 5.2 5.7 + - - -
985 GLN* 3.5 33.4 + - - +
178 ASP* 3.0 32.3 + - - -
208 LYS* 3.0 18.1 - - - +
978 ARG* 3.5 6.0 - - - +
109 PRO* 4.1 1.8 - - - -
399 PRO* 4.1 0.8 - - - +
409 GLN* 2.7 54.5 + - + +
839 ARG* 4.1 29.2 - - - +
849 ALA* 1.3 74.8 - - - +
869 ASN* 1.3 68.6 - - - +
899 GLY 3.6 4.3 - - - +
909 GLU* 3.1 23.6 + - + -
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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