Contacts of the strand formed by residues 799 - 803 (chain B) in PDB entry 1M2V
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 LEU 799 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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758B SER* 3.5 0.9 - - - -
759B LEU* 2.6 53.9 + - + -
760B HIS* 3.1 21.8 + - + +
798B GLY* 1.3 72.1 - - - -
800B TYR* 1.3 60.4 + - - +
810B LEU* 4.1 26.7 - - + -
811B TRP 3.5 3.1 - - - +
812B MET* 3.4 45.5 - - + -
848B PHE* 4.6 12.3 - - + -
852B VAL* 4.3 20.0 - - + -
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Residues in contact with TYR 800 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
756B VAL* 4.7 1.3 - - + -
757B TYR 3.3 5.2 - - - +
758B SER* 3.5 31.9 - - - -
759B LEU* 4.9 0.9 - - - -
760B HIS* 3.3 10.6 + + - -
787B ILE* 4.1 17.5 - - + -
793B LEU 2.8 15.2 + - - -
794B PHE* 3.3 47.6 - + + -
795B GLU* 2.4 47.5 + - - +
798B GLY 3.8 17.0 - - - -
799B LEU* 1.3 75.5 - - - +
801B LEU* 1.3 62.2 + - - +
802B ILE 4.1 0.7 - - - -
810B LEU* 3.2 13.3 - - - +
811B TRP* 2.8 45.6 + + + +
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Residues in contact with LEU 801 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
755B ASP 3.4 0.2 - - - +
756B VAL* 4.5 0.2 - - - -
757B TYR* 2.8 47.1 + - + +
759B LEU* 4.1 18.6 - - + -
800B TYR* 1.3 75.1 - - - +
802B ILE* 1.3 58.8 + - - +
808B LEU* 3.4 24.2 - - + -
809B PHE 3.0 25.8 - - - +
810B LEU* 4.0 11.7 - - + -
852B VAL 5.8 0.2 - - - +
855B ILE* 3.7 21.5 - - + -
856B ILE* 4.2 13.9 - - + -
859B LEU* 3.6 25.1 - - + -
871B LEU* 4.3 9.0 - - + -
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Residues in contact with ILE 802 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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754B PRO* 4.0 17.0 - - + -
755B ASP 3.8 2.9 - - - -
756B VAL* 4.2 7.9 - - + +
794B PHE* 4.0 24.7 - - + -
800B TYR 4.1 0.4 - - - -
801B LEU* 1.3 73.9 - - - +
803B ASP* 1.3 64.8 + - - +
804B ASN 4.2 1.8 - - - +
808B LEU* 2.9 21.0 - - - +
809B PHE* 2.9 41.7 + - + -
811B TRP* 5.8 3.8 - - + -
898B ALA* 3.7 12.8 - - + +
901B THR* 3.1 37.2 - - + +
902B LEU* 3.4 22.4 - - + -
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Residues in contact with ASP 803 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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750B LYS* 2.9 31.7 + - - +
754B PRO* 3.4 3.5 - - - +
755B ASP* 3.0 42.5 + - + +
757B TYR* 4.4 2.0 - - + -
802B ILE* 1.3 77.1 - - - +
804B ASN* 1.3 58.5 + - - +
805B GLY 3.0 7.8 + - - -
807B GLU 4.2 1.6 - - - -
808B LEU* 3.7 13.7 - - + -
859B LEU* 4.2 24.5 - - + +
869B GLN* 2.6 30.6 + - - -
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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
------------------------------------------------------------
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