Contacts of the strand formed by residues 84 - 90 (chain F) in PDB entry 3H2V
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 LEU 84 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76F HIS* 4.1 30.5 - - + +
79F LEU* 4.0 35.2 - - + +
82F TYR* 3.6 5.9 + - + +
83F GLU* 1.3 74.8 - - - +
85F LYS* 1.3 63.1 + - - +
86F TYR 4.3 4.7 - - - +
87F CYS* 4.0 22.4 - - + -
98F VAL* 3.7 22.7 - - + -
99F THR 3.7 3.4 - - - -
100F LEU* 3.4 23.6 - - + -
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Residues in contact with LYS 85 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59F ARG* 4.1 18.8 - - - +
83F GLU* 3.1 49.3 + - - +
84F LEU* 1.3 74.9 - - - +
86F TYR* 1.3 63.0 + - - +
99F THR* 2.8 20.5 + - + +
100F LEU 4.1 7.0 - - - +
101F LEU* 3.9 13.6 - - + +
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Residues in contact with TYR 86 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84F LEU* 3.4 2.4 - - - +
85F LYS* 1.3 83.4 - - - +
87F CYS* 1.3 68.0 + - - +
88F PHE* 3.5 35.0 - - + +
97F PHE* 3.5 24.0 - - + -
98F VAL* 3.0 11.6 - - - +
99F THR* 2.9 51.0 + - + +
128F GLN* 6.1 1.6 - - - -
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Residues in contact with CYS 87 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72F ASN* 5.2 3.9 - - - +
75F VAL* 3.7 32.3 - - - -
76F HIS* 4.0 23.2 + - + +
84F LEU* 4.0 22.2 - - + -
86F TYR* 1.3 86.5 - - - +
88F PHE* 1.3 64.1 + - - +
89F VAL* 4.4 9.8 + - - -
96F ALA* 5.1 0.7 - - - -
97F PHE 3.5 2.9 - - - -
98F VAL* 4.2 8.7 - - - -
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Residues in contact with PHE 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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1052A ALA* 6.5 1.1 - - + -
86F TYR* 3.5 31.0 - - + +
87F CYS* 1.3 76.1 - - - +
89F VAL* 1.3 82.6 + - - +
90F ASP* 4.3 17.3 - - + -
96F ALA* 3.2 1.7 - - - -
97F PHE* 2.7 57.2 + + + +
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Residues in contact with VAL 89 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66F LEU* 5.0 2.5 - - + -
70F VAL* 4.0 25.6 - - + +
71F THR 4.8 0.2 - - - +
72F ASN* 3.4 32.8 + - - +
75F VAL* 3.4 34.5 - - + -
87F CYS* 4.6 5.8 - - - -
88F PHE* 1.3 90.0 - - - +
90F ASP* 1.3 63.7 + - - +
91F LYS* 3.6 26.4 + - + +
95F THR 3.8 3.8 - - - +
96F ALA* 3.8 12.1 - - + -
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Residues in contact with ASP 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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88F PHE* 3.9 18.0 + - + -
89F VAL* 1.3 74.2 - - - +
91F LYS* 1.3 57.2 + - - +
92F TYR* 3.3 18.2 + - - +
93F LYS* 3.1 27.3 + - - +
94F GLY* 2.8 27.4 + - - -
95F THR* 2.7 31.3 + - - +
97F PHE* 4.9 5.1 - - + -
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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