Contacts of the strand formed by residues 88 - 98 (chain F) in PDB entry 1Y18
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 88 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38F ARG* 4.2 9.6 - - + +
39F GLN 3.2 31.0 - - - +
40F ALA* 3.4 7.2 - - + +
41F PRO* 4.6 3.1 - - - -
85F GLU 5.4 0.2 - - - +
86F ASP 3.2 9.2 + - - +
87F SER* 1.3 76.2 - - - +
89F LEU* 1.3 62.3 + - - +
90F TYR* 3.3 16.9 - - + -
108F SER* 4.7 1.6 - - - -
109F VAL 2.9 29.5 + - - -
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Residues in contact with LEU 89 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42E HIS* 3.7 31.4 - - + +
38F ARG* 3.1 3.6 - - - -
39F GLN* 2.9 38.0 + - - +
88F ALA* 1.3 75.4 - - - +
90F TYR* 1.3 61.4 + - - +
91F TYR* 3.1 36.3 - - + +
105F GLN 4.8 2.7 - - - +
106F GLY 4.6 4.9 - - - +
107F THR 3.8 7.4 - - - +
108F SER* 3.6 33.4 - - - +
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Residues in contact with TYR 90 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6F GLU* 3.9 3.5 - - - +
20F LEU* 3.5 20.2 - - + -
36F TRP* 4.4 5.3 - - + -
37F VAL 3.7 2.0 - - - -
38F ARG* 3.3 27.6 + - + +
48F ILE* 3.7 25.4 - - + -
67F PHE* 4.1 4.4 - + - -
80F LEU* 3.6 20.0 - - + -
82F LEU* 4.0 24.5 - - + +
86F ASP* 2.7 34.7 + - - +
88F ALA* 3.3 21.3 - - + -
89F LEU* 1.3 72.5 - - - +
91F TYR* 1.3 62.3 + - - +
106F GLY* 3.1 2.5 - - - -
107F THR* 3.0 35.8 + - + +
109F VAL* 3.8 21.3 - - + -
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Residues in contact with TYR 91 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42E HIS* 3.5 13.2 + - + +
44E PHE* 3.7 22.5 - + - -
6F GLU* 3.5 1.8 - - - +
35F THR 3.8 0.2 - - - +
36F TRP* 3.2 12.8 - - - -
37F VAL 2.5 47.3 + - - +
38F ARG* 4.4 1.3 - - - -
39F GLN* 3.1 34.4 + - + -
45F LEU* 4.3 3.4 - - + -
89F LEU* 3.1 39.6 - - + +
90F TYR* 1.3 71.7 - - - +
92F CYS* 1.3 59.2 + - - +
93F VAL* 3.9 2.4 + - + -
103F TRP* 4.0 26.9 - + + -
104F GLY 3.5 11.2 - - - +
105F GLN 3.3 20.9 - - - -
106F GLY* 3.4 18.4 - - - -
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Residues in contact with CYS 92 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4F LEU* 3.3 9.2 - - + +
6F GLU* 2.9 24.4 + - + +
22F CYS* 2.0 52.3 - - + -
34F MET* 4.1 10.8 - - - -
35F THR 3.8 3.4 - - - -
36F TRP* 4.0 6.1 - - + -
78F LEU* 3.7 17.7 - - - -
91F TYR* 1.3 72.5 - - - +
93F VAL* 1.3 60.3 + - - +
104F GLY 2.9 25.6 + - - -
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Residues in contact with VAL 93 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34F MET* 3.6 8.5 - - - +
35F THR* 2.7 51.4 + - - +
37F VAL* 4.3 6.7 - - + -
91F TYR* 4.1 10.5 - - + +
92F CYS* 1.3 81.9 - - - +
94F ARG* 1.3 70.8 + - - +
100F LEU* 3.6 29.8 - - - -
102F TYR 3.3 11.9 - - - +
103F TRP* 3.3 43.3 - - + +
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Residues in contact with ARG 94 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2F VAL* 4.2 5.3 - - - +
4F LEU* 3.8 7.6 - - + +
27F PHE* 3.4 44.6 - - + +
32F TYR* 3.1 58.9 + - + -
33F TRP 4.0 1.6 - - - +
34F MET* 4.0 15.7 - - + -
93F VAL* 1.3 73.9 - - - +
95F LEU* 1.3 62.0 + - - +
96F ASP* 5.3 0.6 + - - -
100F LEU* 3.5 5.9 + - - -
101F ASP* 2.7 66.7 + - - +
102F TYR* 2.9 38.4 + - + +
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Residues in contact with LEU 95 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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801E HAN 4.0 34.3 - - + +
32F TYR* 3.8 6.1 - - - -
33F TRP* 3.0 48.3 + - + +
35F THR* 3.6 22.2 - - - +
50F ASP* 4.3 8.3 - - - +
93F VAL 3.8 0.8 + - - -
94F ARG* 1.3 75.5 - - - +
96F ASP* 1.3 63.5 + - - +
97F PHE* 3.2 24.7 + - + -
100F VAL* 3.4 46.0 - - + +
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Residues in contact with ASP 96 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56E PRO* 5.6 3.5 - - - +
32F TYR* 3.7 21.7 + - - -
94F ARG* 4.0 1.4 + - - -
95F LEU* 1.3 71.7 - - - +
97F PHE* 1.3 60.5 + - - +
98F ASP* 5.4 1.5 - - - +
100F VAL* 2.8 78.4 + - + +
101F ASP* 3.3 22.4 + - + +
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Residues in contact with PHE 97 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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801E HAN 4.0 44.4 - + + -
32F TYR* 5.4 1.4 - - - -
33F TRP* 3.4 65.7 - + + -
95F LEU* 3.2 16.9 + - + +
96F ASP* 1.3 75.1 + - - +
98F ASP* 1.3 62.8 + - - +
99F VAL* 4.3 19.5 + - + -
100F TYR* 3.8 19.7 - - + -
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Residues in contact with ASP 98 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96F ASP* 5.4 2.0 - - - +
97F PHE* 1.3 73.5 - - - +
99F VAL* 1.3 57.6 + - - +
100F TYR* 2.7 122.4 + - + +
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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