Contacts of the strand formed by residues 4136 - 4141 (chain D) 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 VAL4136 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4097D LEU* 3.5 22.6 - - + +
4101D GLY* 4.1 9.9 + - - +
4103D VAL* 3.7 33.0 - - + -
4131D LEU* 4.4 15.7 - - + +
4134D GLU* 4.8 3.8 - - + -
4135D GLU* 1.3 77.5 - - - +
4137D VAL* 1.3 64.8 + - - +
4138D GLN 3.8 16.2 - - - +
4139D MET* 4.0 11.9 - - + -
4148D VAL* 4.1 23.6 - - + -
4149D VAL 3.5 11.2 - - - +
4150D THR* 4.1 10.5 - - + +
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Residues in contact with VAL4137 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4083D GLN* 2.9 23.5 + - - +
4097D LEU* 3.9 4.0 - - - +
4135D GLU* 3.5 11.4 + - + +
4136D VAL* 1.3 78.6 - - - +
4138D GLN* 1.3 66.5 + - + +
4149D VAL* 2.9 22.5 + - + +
4150D THR 3.7 15.5 - - - +
4151D SER* 3.8 18.6 - - - +
4189D GLY 5.4 3.1 - - - +
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Residues in contact with GLN4138 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4083D GLN* 3.8 13.2 - - - +
4136D VAL* 3.8 2.7 - - - +
4137D VAL* 1.3 84.8 - - + +
4139D MET* 1.3 83.4 + - - +
4140D SER* 4.5 0.4 - - - -
4148D VAL* 3.4 2.8 - - - +
4149D VAL* 3.0 38.2 + - + +
4189D GLY 4.5 7.0 - - - +
4190D GLN* 3.3 25.1 - - + +
4191D VAL* 2.7 53.6 + - - +
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Residues in contact with MET4139 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4083D GLN* 3.7 33.1 - - + +
4084D LEU* 4.1 1.8 - - - -
4085D VAL* 3.4 26.2 - - + +
4095D MET* 3.6 52.0 - - + +
4097D LEU* 3.7 24.9 - - + +
4103D VAL* 4.1 15.0 - - - -
4136D VAL* 4.0 13.5 - - + -
4138D GLN* 1.3 99.4 + - - +
4140D SER* 1.3 62.5 + - - +
4147D ALA 3.5 6.5 - - - +
4148D VAL* 4.1 4.3 - - + -
4191D VAL* 4.7 0.7 - - - -
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Residues in contact with SER4140 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4085D VAL* 4.2 4.9 - - - -
4095D MET* 3.3 9.6 - - - +
4138D GLN* 4.5 0.2 - - - -
4139D MET* 1.3 75.8 - - - +
4141D CYS* 1.3 61.6 + - - +
4142D GLY 4.0 0.2 - - - -
4146D SER* 3.6 1.4 - - - -
4147D ALA 3.0 31.9 + - - -
4191D VAL* 3.4 23.3 - - - +
4192D ALA* 3.4 7.2 - - - +
4193D CYS* 2.9 35.3 + - - +
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Residues in contact with CYS4141 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4085D VAL* 3.7 32.4 - - - +
4086D THR 3.8 6.4 - - - +
4087D SER* 3.6 25.2 - - - +
4088D CYS 4.9 1.2 + - - -
4093D HIS* 3.7 39.7 - - + +
4095D MET* 3.8 18.8 - - - -
4140D SER* 1.3 73.2 + - - +
4142D GLY* 1.3 59.7 + - - +
4145D HIS 3.9 4.5 - - - -
4146D SER* 4.7 0.2 - - - +
4193D CYS* 3.8 9.0 - - - +
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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