Contacts of the strand formed by residues 4048 - 4052 (chain A) in PDB entry 4O2W
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 VAL4048 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4040A PHE* 4.6 0.7 - - + -
4041A VAL 3.2 10.5 - - - +
4042A ILE* 4.3 6.7 - - + -
4046A GLY 3.8 0.9 - - - +
4047A THR* 1.3 80.7 - - - +
4049A LEU* 1.3 68.8 + - - +
4072A VAL* 3.5 7.1 - - - +
4073A ILE* 2.9 46.1 + - + +
4076A LEU* 4.2 16.6 - - + +
4077A GLN* 4.8 0.8 + - - -
4081A VAL* 3.6 43.3 - - + -
4084A LEU* 3.6 25.4 - - + -
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Residues in contact with LEU4049 (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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4040A PHE* 3.2 7.1 - - - +
4041A VAL* 2.9 42.6 + - + +
4043A GLN* 3.6 36.1 - - + +
4047A THR* 4.0 10.5 - - + +
4048A VAL* 1.3 82.0 - - - +
4050A ALA* 1.3 62.3 + - - +
4070A LEU* 4.0 34.3 - - + +
4071A THR 3.2 11.7 - - - +
4072A VAL* 3.8 28.0 - - + +
4073A ILE* 4.5 0.7 - - - -
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Residues in contact with ALA4050 (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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4039A THR 3.3 7.0 - - - +
4040A PHE* 3.5 28.0 - - + -
4049A LEU* 1.3 76.3 - - - +
4051A CYS* 1.3 62.6 + - - +
4059A LEU* 3.9 28.0 - - + +
4061A GLN* 4.3 1.8 - - - +
4067A LEU* 4.3 2.4 - - - +
4069A VAL 3.5 2.3 - - - +
4070A LEU* 3.5 3.8 - - - -
4071A THR* 2.9 33.5 + - - +
4073A ILE* 4.3 4.3 - - + -
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Residues in contact with CYS4051 (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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4008A GLY 3.6 16.6 - - - +
4009A GLN 3.7 16.8 - - - -
4011A ALA* 4.5 4.0 - - - -
4026A PHE* 4.1 11.2 - - - -
4038A CYS* 3.4 6.2 - - - +
4039A THR 2.9 34.1 + - - +
4050A ALA* 1.3 76.7 - - - +
4052A GLY* 1.3 60.8 - - - +
4059A LEU* 3.6 9.8 - - - +
4067A LEU* 3.5 13.7 - - - +
4069A VAL 3.6 17.7 - - - +
4070A LEU* 3.8 20.0 - - - +
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Residues in contact with GLY4052 (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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4007A HIS 3.2 18.3 - - - +
4008A GLY 3.9 0.2 + - - -
4009A GLN* 3.6 11.7 - - - -
4037A ASN 3.5 8.7 - - - -
4051A CYS* 1.3 76.4 - - - +
4053A GLU* 1.3 66.2 + - - -
4059A LEU* 3.5 3.0 - - - +
4066A ASP* 3.4 2.6 - - - -
4067A LEU 2.7 35.8 + - - -
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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