Contacts of the strand formed by residues 764 - 769 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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723A LYS 3.4 2.4 - - - +
724A VAL* 3.6 1.9 - - - -
725A ILE* 2.7 41.9 + - + +
734A PHE* 3.3 34.0 - - + -
741A MET* 3.0 38.1 - - + -
758A LEU* 3.2 17.3 - - + -
759A CYS 3.9 5.8 - - - +
760A PRO* 4.2 8.5 - - + -
763A SER* 1.3 74.3 - - - +
765A GLN* 1.3 62.1 + - - +
766A LEU* 3.8 22.6 + - + -
839A LEU* 3.8 26.0 - - + -
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Residues in contact with GLN 765 (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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687A GLU* 2.9 25.9 - - - +
690A LEU* 4.2 11.7 - - + +
692A LYS* 3.0 39.8 - - - +
722A ILE* 3.4 20.1 - - + +
723A LYS 3.4 3.8 - - - -
724A VAL* 4.0 8.4 - - + +
758A LEU* 3.8 6.1 - - - +
759A CYS* 3.1 53.7 + - + +
763A SER* 4.5 8.1 - - - +
764A LEU* 1.3 76.6 - - - +
766A LEU* 1.3 63.9 + - - +
767A VAL* 3.8 2.5 + - - +
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Residues in contact with LEU 766 (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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721A CYS 3.5 1.9 - - - +
722A ILE* 3.4 3.1 - - - -
723A LYS* 2.8 51.4 + - + +
725A ILE* 3.6 28.5 - - + -
741A MET* 6.0 1.1 - - + -
744A ILE* 5.5 8.3 - - + -
755A LEU* 3.7 27.8 - - + -
757A GLY 4.2 0.4 - - - -
758A LEU* 3.4 28.5 - - + -
764A LEU* 3.8 13.4 + - + -
765A GLN* 1.3 72.3 - - - +
767A VAL* 1.3 60.8 + - - +
768A THR* 4.0 2.8 + - + +
836A VAL* 4.3 18.8 - - + -
839A LEU* 4.3 9.0 - - + -
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Residues in contact with VAL 767 (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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685A PHE* 4.3 20.0 - - + -
690A LEU* 3.6 44.9 - - + -
709A TRP* 5.8 0.4 - - + -
720A VAL* 4.0 28.0 - - + -
721A CYS 3.4 3.4 - - - +
722A ILE* 4.2 11.2 - - + -
755A LEU* 3.9 1.4 - - - +
756A LEU* 3.1 27.2 + - + +
757A GLY 3.2 18.5 + - - +
759A CYS* 5.4 0.2 - - + -
765A GLN 4.2 7.4 - - - +
766A LEU* 1.3 75.8 - - - +
768A THR* 1.3 64.3 + - - +
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Residues in contact with THR 768 (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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301A ANP 3.5 20.6 + - - -
720A VAL* 3.5 7.1 - - - +
721A CYS* 2.7 41.0 + - - +
753A VAL* 4.0 18.8 - - + +
754A ARG 3.7 17.3 - - - +
755A LEU* 4.0 18.6 - - + -
756A LEU* 4.0 6.7 - - - -
766A LEU* 4.0 2.9 + - + +
767A VAL* 1.3 79.7 - - - +
769A GLN* 1.3 60.2 + - - +
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Residues in contact with GLN 769 (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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301A ANP 2.8 29.6 + - - -
719A PRO 4.7 3.6 - - - +
720A VAL* 4.7 3.4 - - - +
721A CYS 4.3 0.2 - - - -
753A VAL* 4.5 7.4 - - + +
754A ARG* 2.8 44.7 + - - +
756A LEU* 3.5 27.4 - - + +
768A THR* 1.3 73.6 + - - +
770A TYR* 1.3 56.4 - - - +
771A LEU* 3.8 18.9 + - + +
824A LYS* 5.6 8.6 - - + +
830A GLN* 4.7 11.4 + - - +
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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