Contacts of the strand formed by residues 764 - 769 (chain B) in PDB entry 3LMG
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 764 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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723B LYS 3.4 1.4 - - - +
724B VAL* 3.5 2.4 - - - +
725B ILE* 2.8 54.4 + - + +
734B PHE* 3.3 42.0 - - + +
741B MET* 3.2 39.0 - - + -
758B LEU* 5.3 5.4 - - + -
759B CYS 4.0 6.1 - - - +
760B PRO* 5.5 1.8 - - + -
761B GLY 5.1 0.2 - - - +
763B SER* 1.3 73.4 - - - +
765B GLN* 1.3 64.1 + - - +
766B LEU* 3.5 39.7 - - + -
839B LEU* 4.5 9.0 - - + -
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Residues in contact with GLN 765 (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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687B GLU* 3.4 24.4 + - - +
690B LEU* 3.9 14.2 - - + +
692B LYS* 2.9 27.4 + - - +
722B ILE* 3.6 19.8 - - + +
723B LYS 3.3 3.8 - - - -
724B VAL* 4.4 12.3 - - + -
758B LEU* 3.4 6.9 - - - +
759B CYS* 2.9 62.4 + - + +
760B PRO 5.3 0.2 + - - -
761B GLY* 6.2 0.4 - - - -
763B SER* 4.4 7.7 + - - +
764B LEU* 1.3 79.2 - - - +
766B LEU* 1.3 60.5 + - - +
767B VAL* 3.9 1.1 + - - +
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Residues in contact with LEU 766 (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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721B CYS 3.5 1.6 - - - +
722B ILE* 3.3 4.0 - - - -
723B LYS* 2.7 52.6 + - + +
725B ILE* 3.7 20.0 - - + -
744B ILE* 5.2 9.9 - - + -
755B LEU* 3.6 37.0 - - + -
757B GLY 4.3 0.2 - - - -
758B LEU* 4.0 13.5 - - + -
764B LEU* 3.5 24.7 - - + -
765B GLN* 1.3 72.4 - - - +
767B VAL* 1.3 60.1 + - - +
768B THR* 4.1 2.7 + - + -
834B PHE 5.9 0.2 - - - +
836B VAL* 4.3 19.5 - - + -
839B LEU* 5.2 7.4 - - + -
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Residues in contact with VAL 767 (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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685B PHE* 3.5 26.5 - - + -
690B LEU* 3.6 35.9 - - + -
709B TRP* 5.5 0.2 - - + -
720B VAL* 3.9 34.3 - - + -
721B CYS 3.4 4.3 - - - +
722B ILE* 4.2 8.7 - - + -
755B LEU* 3.8 1.3 - - - +
756B LEU* 3.0 26.2 + - + -
757B GLY 3.0 18.6 + - - +
758B LEU* 5.1 0.2 - - - -
765B GLN 4.4 6.1 - - - +
766B LEU* 1.3 77.6 - - - +
768B THR* 1.3 66.9 + - - +
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Residues in contact with THR 768 (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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301B ANP 3.8 17.2 + - - -
720B VAL* 3.6 7.3 - - - +
721B CYS* 2.7 37.3 + - - +
753B VAL* 3.9 18.5 - - + +
754B ARG 3.2 25.4 - - - +
755B LEU* 3.8 20.0 - - + -
756B LEU* 4.1 8.7 - - - +
766B LEU* 4.1 2.7 + - + -
767B VAL* 1.3 77.3 - - - +
769B GLN* 1.3 58.0 + - - +
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Residues in contact with GLN 769 (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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301B ANP 2.7 32.1 + - - -
719B PRO 4.7 4.9 - - - +
721B CYS* 3.8 1.2 - - - +
753B VAL* 4.9 4.0 - - + +
754B ARG* 3.3 44.7 + - + +
756B LEU* 3.7 23.1 - - + +
768B THR* 1.3 77.7 - - - +
770B TYR* 1.3 56.6 + - - +
771B LEU* 4.2 16.6 - - + +
824B LYS* 3.9 22.1 + - - +
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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
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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