Contacts of the strand formed by residues 199 - 203 (chain B) in PDB entry 5M64
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 ILE 199 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130B LEU* 6.4 0.2 - - + -
195B ILE* 3.5 3.9 - - - -
196B VAL* 2.9 40.4 + - + +
197B ASN* 4.1 11.2 - - + +
198B GLY* 1.3 80.5 - - - +
200B GLU* 1.3 70.3 + - - +
201B LYS* 4.7 5.2 - - + +
487B VAL* 4.7 15.9 - - + -
737B SER 5.2 1.6 - - - +
738B ASP* 4.9 2.0 - - + +
739B ASN* 4.7 30.3 - - + +
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Residues in contact with GLU 200 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193B TYR* 3.6 27.8 - - + -
194B PHE 3.7 5.4 - - - -
195B ILE* 3.7 7.0 - - + +
198B GLY 4.6 1.4 - - - +
199B ILE* 1.3 81.0 - - - +
201B LYS* 1.3 66.6 + - - +
487B VAL* 3.6 19.0 - - + +
488B ALA* 2.9 35.1 - - + +
489B GLU* 3.9 7.3 - - - -
490B LYS* 3.8 7.3 - - + +
496B PHE* 6.0 1.3 - - + -
736B ARG* 3.0 30.0 + - - +
738B ASP* 3.8 20.7 - - - +
739B ASN* 5.4 0.7 - - - +
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Residues in contact with LYS 201 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193B TYR* 3.4 5.2 - - - +
194B PHE* 2.8 42.9 + - + +
195B ILE* 5.2 0.2 - - - -
196B VAL* 3.4 35.0 + - - +
199B ILE* 4.7 5.7 - - + +
200B GLU* 1.3 79.9 - - - +
202B LEU* 1.3 61.2 + - - +
465B LEU* 3.1 56.7 - - + +
466B SER* 3.3 13.1 - - - +
485B THR* 3.2 23.3 - - + +
486B VAL 3.8 9.2 - - - +
487B VAL* 4.4 12.1 - - + +
488B ALA* 5.2 1.8 - - - +
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Residues in contact with LEU 202 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45B HIS* 4.1 11.0 - - + +
192B GLY 3.6 16.8 - - - +
193B TYR* 4.0 7.0 - - + -
194B PHE* 4.9 1.1 - - - +
201B LYS* 1.3 76.7 - - - +
203B ILE* 1.3 96.6 + - + +
204B ARG* 4.4 3.4 - - - +
465B LEU* 5.9 0.4 - - - -
485B THR* 2.8 17.1 + - - -
486B VAL* 3.0 38.7 + - + +
488B ALA* 5.6 9.0 - - + -
499B HIS* 3.3 29.2 - - + +
500B PHE* 3.6 33.2 - - + -
502B MET* 5.7 1.3 - - + -
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Residues in contact with ILE 203 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45B HIS* 4.6 9.3 + - + +
164B MET* 5.6 8.3 - - + -
192B GLY 5.8 0.9 - - - +
194B PHE* 5.5 13.4 - - + +
202B LEU* 1.3 93.3 - - + +
204B ARG* 1.3 71.2 + - - +
205B MET* 3.6 1.6 + - - -
404B LEU 4.9 2.6 - - - +
405B GLY* 4.1 32.7 - - - +
406B GLY* 4.7 2.7 - - - +
408B LEU* 5.2 8.1 - - + -
409B TYR* 6.1 4.3 - - + -
464B PHE* 4.5 17.3 - - + -
465B LEU* 4.6 19.2 - - + +
484B TYR* 3.2 30.3 - - + +
485B THR* 4.4 3.1 - - - -
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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
------------------------------------------------------------
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