Contacts of the strand formed by residues 163 - 166 (chain F) in PDB entry 4R8A
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 VAL 163 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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73F LEU* 4.7 4.0 - - + -
74F PHE 3.3 14.4 - - - +
75F ARG* 3.8 28.5 - - + -
102F ALA* 3.7 7.3 - - - +
103F GLN 4.1 1.3 + - - +
104F PRO* 3.3 36.3 - - + +
106F LEU* 4.8 1.1 - - + -
114F LEU* 3.6 28.9 - - + -
115F LEU* 6.0 0.2 - - + -
152F LEU* 3.5 29.6 - - + +
159F PHE* 4.4 7.0 - - + -
161F GLU* 3.7 1.6 + - + -
162F PRO* 1.3 73.2 - - - +
164F TYR* 1.3 64.3 + - - +
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Residues in contact with TYR 164 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66F MET* 4.0 9.2 - - + -
72F THR 3.6 2.9 - - - +
73F LEU* 3.6 0.5 - - - -
74F PHE* 2.7 44.9 + - + +
76F GLU* 2.6 45.4 + - + -
79F LEU* 4.2 17.3 - - + -
87F THR* 4.7 6.5 - - + -
88F ARG* 3.9 9.2 - - - +
91F VAL* 3.8 40.6 - - + +
92F GLN* 5.4 0.3 + - - -
95F LEU* 4.3 10.8 - - + -
100F VAL* 3.6 14.8 - - + -
101F ASP 4.0 1.6 - - - -
102F ALA* 3.9 28.0 - - + -
162F PRO* 3.5 16.9 - - + +
163F VAL* 1.3 75.0 - - - +
165F GLU* 1.3 59.3 + - - +
166F LEU 4.0 0.2 + - - -
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Residues in contact with GLU 165 (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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72F THR* 3.3 13.9 - - + +
73F LEU* 3.8 20.1 - - + +
100F VAL* 3.2 5.5 - - - -
101F ASP* 2.7 45.2 + - + +
104F PRO* 3.3 27.7 - - + +
105F THR 5.0 4.2 + - - +
106F LEU* 5.6 0.2 - - - +
110F GLN* 5.9 1.0 + - - -
164F TYR* 1.3 72.5 - - - +
166F LEU* 1.3 74.2 + - - +
167F ARG* 2.7 34.9 + - + +
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Residues in contact with LEU 166 (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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63F LEU* 3.7 27.4 - - + -
66F MET* 3.7 25.9 - - + +
67F VAL* 3.7 39.7 - - + +
72F THR* 2.6 43.6 + - - +
99F TRP 3.6 14.1 - - - +
100F VAL* 4.2 5.2 - - + -
164F TYR 4.0 0.8 + - - -
165F GLU* 1.3 75.6 - - - +
167F ARG* 1.3 59.5 + - - +
168F CYS* 3.7 14.5 + - - +
169F MET* 3.9 21.6 + - + +
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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