Contacts of the strand formed by residues 79 - 83 (chain A) in PDB entry 4Y6O
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 79 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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71A MET* 5.1 3.1 - - + -
76A CYS* 4.1 14.8 - - - -
78A ARG* 1.3 79.0 - - - +
80A ILE* 1.3 73.0 + - - +
81A CYS* 4.1 0.4 - - - -
155A LEU* 4.4 23.6 - - + -
160A LEU* 2.7 33.7 + - + +
161A LEU* 3.7 5.9 - - - +
162A LEU 2.8 27.6 + - - +
163A ARG 3.7 1.4 + - - -
256A LEU* 3.4 39.9 - - + +
258A LEU* 4.4 11.9 - - + -
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Residues in contact with ILE 80 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79A VAL* 1.3 73.4 - - - +
81A CYS* 1.3 68.5 + - - +
82A LEU* 4.0 13.4 - - + +
162A LEU* 3.8 17.3 - - + -
163A ARG* 3.3 8.7 - - + +
165A TYR* 3.7 28.7 - - + -
250A ASP* 3.6 39.9 - - + +
251A PHE* 3.9 20.9 - - + -
254A VAL* 3.7 18.3 - - + +
256A LEU 3.0 6.9 + - - +
257A LEU* 3.4 11.8 - - + -
258A LEU* 2.9 25.3 + - - +
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Residues in contact with CYS 81 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79A VAL* 4.1 1.5 - - - -
80A ILE* 1.3 75.8 - - - +
82A LEU* 1.3 60.0 - - - +
83A VAL* 4.1 4.0 - - + -
152A MET* 3.6 34.8 - - - -
155A LEU* 3.6 30.3 - - - -
161A LEU* 3.9 8.7 - - - -
163A ARG 2.9 10.1 + - - +
164A CYS* 3.4 5.3 - - - -
165A TYR 2.8 31.9 + - - -
258A LEU* 3.3 22.4 - - - +
260A MET* 4.2 0.9 - - - -
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Residues in contact with LEU 82 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80A ILE* 4.0 16.4 - - + +
81A CYS* 1.3 74.8 - - - +
83A VAL* 1.3 60.6 + - - +
165A TYR* 3.4 10.3 - - + -
251A PHE* 4.0 10.1 - - + -
257A LEU* 3.9 25.4 - - + -
258A LEU 2.8 9.2 + - - +
259A VAL* 3.3 17.3 - - + -
260A MET 2.8 26.2 + - - +
262A THR* 4.0 4.9 - - - +
264A LEU* 5.3 1.1 - - + -
269A PHE* 4.1 13.7 - - + +
272A LEU* 3.7 43.1 - - + -
273A ILE* 3.8 24.0 - - + -
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Residues in contact with VAL 83 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81A CYS* 4.4 0.4 - - + -
82A LEU* 1.3 81.2 - - - +
84A GLY* 1.3 59.0 + - - +
87A ILE* 3.8 25.4 - - + -
152A MET* 3.8 26.5 - - + -
164A CYS* 4.0 8.7 - - - -
165A TYR 2.9 11.2 + - - +
166A THR* 3.5 28.9 - - - +
167A GLN* 3.0 36.5 + - - +
168A ASN* 5.0 0.2 - - - +
173A GLU* 3.9 2.2 - - - +
260A MET* 3.2 28.9 - - + +
262A THR* 4.2 0.9 - - - -
269A PHE* 3.9 1.2 - - - -
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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