Contacts of the strand formed by residues 83 - 89 (chain O) in PDB entry 1UW9
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 ARG 83 (chain O).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23O THR 5.7 0.2 - - - +
24O TYR 3.8 3.8 - - - -
26O THR* 3.2 35.1 + - + +
29O TYR* 3.6 54.9 + - + +
78O ASP* 3.0 37.0 + - - +
81O LYS* 3.7 34.7 + - + +
82O GLY* 1.3 79.2 - - - +
84O CYS* 1.3 60.5 + - - +
85O TYR* 3.2 7.5 + - - +
101O VAL* 3.2 6.8 - - - +
102O ALA* 2.9 36.6 + - + +
104O HYP 4.8 5.2 + - - -
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Residues in contact with CYS 84 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24O TYR 2.8 16.6 + - - +
25O TYR* 3.4 14.0 - - + -
26O THR 2.9 25.4 + - - -
54O GLY* 3.7 35.4 - - - +
55O ALA 4.1 1.1 - - - +
58O ALA* 3.6 6.4 - - + +
83O ARG* 1.3 68.7 - - - +
85O TYR* 1.3 57.3 + - - +
86O ASP 4.0 2.9 - - - -
87O ILE* 3.7 35.9 - - - -
99O ALA* 4.3 6.5 - - - -
100O TYR 3.2 15.0 - - - +
101O VAL* 4.3 2.0 - - + +
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Residues in contact with TYR 85 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25O TYR* 5.2 0.9 - - - -
26O THR* 3.3 17.5 - - - +
27O PRO* 3.5 25.2 - - - +
29O TYR* 4.1 24.4 - - + +
31O VAL* 3.6 27.5 - - + +
37O LEU* 3.8 21.7 - - + +
83O ARG 3.2 11.8 + - - +
84O CYS* 1.3 73.7 - - - +
86O ASP* 1.3 70.3 + - + +
100O TYR* 2.9 35.7 + + + +
101O VAL 3.6 21.7 + - - -
102O ALA* 3.6 12.8 - - + -
364O PHE* 3.9 11.6 - - - -
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Residues in contact with ASP 86 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25O TYR* 5.0 2.9 - - - -
27O PRO* 5.5 1.1 - - - -
84O CYS* 3.6 2.7 + - - -
85O TYR* 1.3 98.1 - - + +
87O ILE* 1.3 79.0 + - - +
88O GLU* 4.8 8.0 - - - +
99O ALA* 3.6 0.2 - - - -
100O TYR* 2.8 51.7 + - + +
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Residues in contact with ILE 87 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25O TYR* 3.7 22.6 + - + +
42O MET* 4.6 3.8 - - + -
50O PRO* 3.5 31.2 - - + +
51O GLU* 3.6 22.0 - - + +
54O GLY* 4.8 0.9 - - - -
84O CYS* 3.7 17.7 - - - -
86O ASP* 1.3 88.5 + - - +
88O GLU* 1.3 62.2 + - - +
89O PRO* 4.0 5.5 - - - +
97O TYR* 3.8 35.0 - - + -
98O ILE 3.3 5.2 - - - +
99O ALA* 4.5 4.5 - - + -
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Residues in contact with GLU 88 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86O ASP* 4.3 8.4 - - - +
87O ILE* 1.3 73.2 - - - +
89O PRO* 1.3 73.3 - - + +
97O TYR* 3.2 6.9 - - - -
98O ILE* 2.7 51.1 + - + +
100O TYR* 3.0 29.9 + - + -
356O LYS* 5.3 5.5 + - - -
358O ARG* 2.9 33.7 + - - -
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Residues in contact with PRO 89 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87O ILE 4.0 6.1 - - - +
88O GLU* 1.3 94.5 - - + +
90O VAL* 1.3 63.9 + - - +
91O PRO* 3.6 8.2 - - - +
93O GLU 5.9 1.3 - - - +
96O GLN 4.1 0.4 - - - +
97O TYR* 4.0 21.5 - - + -
98O ILE* 5.4 0.7 - - - +
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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