Contacts of the strand formed by residues 85 - 92 (chain F) in PDB entry 2J0Q
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 85 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10F TYR* 4.0 23.6 + - + -
11F VAL* 3.3 7.1 - - - +
12F GLY 3.0 29.2 + - - +
14F LYS* 5.7 5.9 - - - +
19F HIS* 5.7 1.0 + - - -
80F PRO* 3.9 21.0 - - + +
84F GLY* 1.3 74.3 - - - -
86F GLN* 1.3 70.9 + - - +
87F GLU* 3.0 30.5 + - + -
100F THR* 3.7 29.2 - - + -
101F THR 3.4 3.6 - - - -
102F SER* 4.2 2.9 - - - +
103F LYS* 4.6 1.0 - - - +
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Residues in contact with GLN 86 (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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9F TYR* 2.6 39.3 + - + +
10F TYR 3.4 8.1 - - - +
11F VAL* 3.9 10.1 - - + -
85F ARG* 1.3 72.3 - - - +
87F GLU* 1.3 62.5 + - - +
99F PHE 3.6 0.7 - - - +
100F THR* 3.2 8.0 - - - +
101F THR* 2.4 52.7 + - + +
102F SER 3.1 16.4 - - - +
103F LYS* 3.8 9.4 - - - -
104F ILE* 3.9 13.2 + - - +
122F PHE* 3.6 26.2 - - + -
126F VAL* 3.7 8.7 - - - +
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Residues in contact with GLU 87 (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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8F ARG* 3.1 36.2 + - - +
9F TYR* 3.2 9.7 - - - -
10F TYR* 2.8 55.1 + - + +
85F ARG* 3.0 35.5 + - - -
86F GLN* 1.3 75.5 - - - +
88F LEU* 1.3 59.2 + - - +
89F GLU 4.2 0.4 - - - -
98F SER* 6.2 0.2 - - - +
99F PHE 3.4 4.5 - - - +
100F THR* 4.3 10.1 - - - +
122F PHE* 5.3 0.7 - - - -
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Residues in contact with LEU 88 (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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7F LEU* 3.8 12.3 - - + -
8F ARG 3.5 2.7 - - - +
9F TYR* 4.0 17.7 - - + -
69F ILE* 4.6 0.7 - - + -
86F GLN 4.3 0.2 - - - -
87F GLU* 1.3 72.1 - - - +
89F GLU* 1.3 60.5 + - - +
90F ILE* 3.8 27.1 - - + -
97F ILE* 4.3 0.7 - - - +
98F SER* 3.2 3.6 - - - -
99F PHE* 2.7 57.3 + - + +
122F PHE* 3.8 27.3 - - + -
125F LEU* 4.3 19.5 - - + -
126F VAL* 5.0 3.6 - - + -
129F LEU* 3.6 28.3 - - + -
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Residues in contact with GLU 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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6F TYR* 4.2 19.3 + - + -
7F LEU* 3.3 2.1 - - - +
8F ARG* 2.9 74.2 + - + +
87F GLU 4.2 0.6 - - - -
88F LEU* 1.3 71.7 - - - +
90F ILE* 1.3 68.9 + - - +
91F VAL 4.4 0.2 - - - -
96F HIS* 3.2 29.0 + - - +
97F ILE 3.6 9.0 - - - +
98F SER* 4.3 12.3 - - - +
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Residues in contact with ILE 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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5F PHE* 4.3 10.8 - - + -
6F TYR 3.4 11.7 - - - +
7F LEU* 4.3 12.1 - - + -
64F ILE* 4.1 34.1 - - + -
69F ILE* 4.3 6.1 - - + -
70F THR* 5.7 0.4 - - + -
88F LEU* 3.8 25.1 - - + -
89F GLU* 1.3 80.1 - - - +
91F VAL* 1.3 66.0 + - - +
92F ILE* 3.7 27.7 + - + -
95F GLU 4.0 0.3 - - - +
96F HIS* 3.5 1.6 - - - -
97F ILE* 2.8 63.5 + - + +
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Residues in contact with VAL 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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4F ASP* 3.5 9.6 - - + +
5F PHE 3.5 0.4 - - - -
6F TYR* 2.9 57.5 + - + -
90F ILE* 1.3 72.7 - - - +
92F ILE* 1.3 57.3 + - - +
93F GLY 3.9 16.8 - - - +
94F ASP 5.5 0.4 - - - +
95F GLU 3.5 11.4 - - - +
96F HIS* 3.8 36.1 - - + +
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Residues in contact with ILE 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 ASP 4.0 3.1 - - - -
5F PHE* 4.0 16.4 - - + -
61F LYS* 3.5 28.5 - - + -
64F ILE* 4.6 9.6 - - + -
65F ASP* 3.4 25.1 - - - +
70F THR* 4.5 9.0 - - + -
90F ILE* 3.9 20.4 - - + +
91F VAL* 1.3 70.5 - - - +
93F GLY* 1.3 59.1 + - - +
94F ASP 3.7 3.2 + - - -
95F GLU* 3.3 42.9 + - + +
97F ILE* 5.4 1.1 - - + -
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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