Contacts of the strand formed by residues 86 - 93 (chain B) in PDB entry 2F5Y
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 GLU 86 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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20B THR* 3.4 28.9 - - + -
21B ILE 3.2 15.9 - - - +
22B PRO* 3.8 9.4 - - + -
28B PHE* 4.1 4.5 - - - -
64B ASN* 4.2 5.0 + - - +
83B CYS* 4.0 8.5 + - - +
84B PRO* 5.7 0.2 - - - +
85B SER* 1.3 83.4 + - - +
87B ILE* 1.3 73.0 + - - +
88B ILE* 4.8 7.9 - - + -
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Residues in contact with ILE 87 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19B ILE 4.0 0.5 - - - +
20B THR* 3.5 1.9 - - - +
21B ILE* 2.7 42.0 + - + +
28B PHE* 3.7 35.7 - - + -
30B PHE* 4.2 15.3 - - + -
63B LEU* 3.8 17.7 - - + -
64B ASN* 3.3 5.8 - - - +
80B ILE* 4.3 14.1 - - + +
83B CYS* 3.6 31.2 - - + -
86B GLU* 1.3 79.4 - - - +
88B ILE* 1.3 61.4 + - - +
89B LEU* 3.9 25.8 - - + -
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Residues in contact with ILE 88 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18B GLN* 3.6 38.8 - - + +
19B ILE 3.3 6.3 - - - +
20B THR* 3.7 27.1 - - + +
62B GLN 3.8 0.7 - - - +
63B LEU* 3.6 3.8 - - - +
64B ASN* 2.9 42.5 + - - +
65B GLU 4.7 1.9 + - - +
86B GLU* 4.8 8.1 - - + -
87B ILE* 1.3 76.9 - - - +
89B LEU* 1.3 65.0 + - - +
90B LEU 4.1 0.2 + - - -
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Residues in contact with LEU 89 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17B ARG 3.7 1.0 - - - +
18B GLN* 3.5 3.2 - - - +
19B ILE* 2.7 45.6 + - + +
21B ILE* 4.1 11.0 - - + -
30B PHE* 4.1 25.1 - - + -
54B LEU* 4.1 22.9 - - + -
60B VAL* 4.3 19.5 - - + -
62B GLN 3.3 7.6 - - - +
63B LEU* 3.3 33.2 - - + -
76B LEU* 5.9 0.4 - - + -
80B ILE* 5.0 5.4 - - + -
87B ILE* 3.9 12.8 - - + -
88B ILE* 1.3 75.5 - - - +
90B LEU* 1.3 60.6 + - - +
91B VAL* 4.0 15.4 - - + +
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Residues in contact with LEU 90 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16B TYR* 4.2 29.4 - - + -
17B ARG 3.5 14.1 - - - +
18B GLN* 4.1 21.8 - - + +
60B VAL* 3.8 0.9 - - - -
61B LEU* 2.9 37.8 + - + -
62B GLN* 2.9 45.8 + - + +
88B ILE* 4.1 0.6 + - - +
89B LEU* 1.3 71.3 - - - +
91B VAL* 1.3 64.6 + - - +
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Residues in contact with VAL 91 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16B TYR* 3.3 6.9 - - - +
17B ARG* 2.8 59.3 + - + +
19B ILE* 4.5 6.7 - - + -
54B LEU* 4.2 17.0 - - + -
58B ASP* 3.8 31.0 - - + +
59B THR 3.1 11.7 - - - +
60B VAL* 4.4 9.9 - - + -
61B LEU* 4.4 4.9 - - - -
89B LEU* 4.0 21.8 - - + +
90B LEU* 1.3 79.8 - - - +
92B TRP* 1.3 58.8 + - - +
93B ARG* 4.6 4.3 - - + +
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Residues in contact with TRP 92 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14B MET 5.9 2.7 - - - +
15B ARG 3.4 6.1 - - - +
16B TYR* 4.7 5.2 - - + +
57B LEU 4.1 2.3 - - - +
58B ASP* 3.8 2.4 - - - -
59B THR* 2.8 45.3 + - + +
61B LEU* 4.0 24.6 - - + +
91B VAL* 1.3 71.9 - - - +
93B ARG* 1.3 58.6 + - - +
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Residues in contact with ARG 93 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14B MET 3.2 7.4 + - - +
15B ARG* 2.7 45.0 + - - +
17B ARG* 4.1 17.1 - - + +
19B ILE* 4.1 12.5 - - - +
53B GLY 2.8 28.7 + - - -
54B LEU* 4.1 0.6 - - - +
55B GLN* 3.3 29.3 + - - +
57B LEU 5.2 0.2 - - - -
58B ASP* 2.9 41.8 + - - +
91B VAL* 4.6 7.4 - - + +
92B TRP* 1.3 74.5 - - - +
94B MET* 1.3 69.8 + - - +
95B VAL* 2.7 39.8 - - + +
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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