Contacts of the strand formed by residues 690 - 698 (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 690 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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685A PHE* 4.1 16.6 - - + -
686A LYS 4.4 2.0 - - - +
687A GLU 3.3 16.9 + - - +
688A THR 4.7 2.0 - - - -
689A GLU* 1.3 79.7 + - - +
691A ARG* 1.3 63.5 + - - +
692A LYS* 6.0 0.2 - - - -
708A VAL 3.7 1.8 - - - +
709A TRP* 3.8 25.4 - - + -
710A ILE* 5.4 0.2 - - - -
720A VAL* 4.6 0.7 - - + -
722A ILE* 4.1 16.8 - - + -
759A CYS* 3.9 27.8 - - + -
765A GLN* 4.2 16.8 - - - +
767A VAL* 3.6 44.2 - - + -
728B LYS 4.5 7.3 - - - +
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Residues in contact with ARG 691 (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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689A GLU 4.1 0.2 + - - -
690A LEU* 1.3 74.7 - - - +
692A LYS* 1.3 67.0 + - - +
693A LEU* 3.8 21.9 + - + +
707A GLY* 3.1 2.3 - - - -
708A VAL* 2.7 45.6 + - + +
710A ILE* 4.4 20.2 - - + -
722A ILE* 3.8 2.2 - - - +
728B LYS* 3.7 52.3 + - + +
843B ASP* 3.1 32.7 + - - -
844B ASP 5.6 1.4 + - - -
845B LYS* 3.7 16.2 - - - +
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Residues in contact with LYS 692 (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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690A LEU 6.0 0.2 - - - -
691A ARG* 1.3 75.0 - - - +
693A LEU* 1.3 64.8 + - - +
705A HIS* 3.9 35.8 + - + +
706A LYS 4.0 3.1 - - - -
707A GLY* 4.1 1.3 - - - -
722A ILE* 3.9 18.6 - - + -
724A VAL* 3.4 23.9 - - - +
765A GLN* 3.0 31.5 - - - +
703B THR* 6.0 0.4 - - - +
726B GLU* 3.0 39.5 + - - +
728B LYS* 3.1 30.3 + - - +
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Residues in contact with LEU 693 (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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691A ARG* 4.2 23.8 - - + +
692A LYS* 1.3 79.1 - - - +
694A LYS* 1.3 62.9 + - + +
706A LYS* 2.8 24.3 + - + +
707A GLY* 3.6 16.8 - - - +
708A VAL* 3.3 37.7 - - + +
698B SER* 4.8 1.0 + - - -
699B GLY 4.6 10.6 - - - +
728B LYS* 4.7 5.7 + - - +
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Residues in contact with LYS 694 (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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692A LYS 3.9 0.2 - - - -
693A LEU* 1.3 81.9 - - + +
695A VAL* 1.3 73.8 + - + +
696A LEU* 4.4 13.2 - - + -
705A HIS* 3.3 7.0 - - - -
706A LYS* 2.6 54.8 + - + +
698B SER* 4.0 9.9 - - - +
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Residues in contact with VAL 695 (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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694A LYS* 1.3 90.9 - - + +
696A LEU* 1.3 64.2 + - - +
697A GLY 3.9 7.6 - - - +
703A THR* 3.9 6.7 - - + -
704A VAL 3.6 7.6 - - - +
705A HIS* 3.2 36.3 + - + +
695B VAL* 3.8 21.3 - - + -
697B GLY* 3.6 14.6 - - - +
698B SER* 3.3 36.6 + - - +
703B THR* 4.3 0.2 - - + -
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Residues in contact with LEU 696 (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 3.6 45.5 + - + +
694A LYS* 4.4 11.2 - - + -
695A VAL* 1.3 79.3 - - - +
697A GLY* 1.3 59.1 + - - +
704A VAL* 2.9 14.4 + - + +
706A LYS* 4.0 30.5 - - + +
721A CYS* 3.9 15.9 - - - -
770A TYR* 3.8 22.2 - - + +
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Residues in contact with GLY 697 (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 3.7 12.3 - - - -
695A VAL* 3.7 2.4 - - - +
696A LEU* 1.3 81.7 - - - +
698A SER* 1.3 61.9 + - - -
703A THR* 3.6 3.6 - - - +
704A VAL* 2.8 26.9 + - - +
695B VAL* 3.5 16.4 - - - -
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Residues in contact with SER 698 (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 3.6 11.9 + - - -
697A GLY* 1.3 75.8 - - - -
699A GLY* 1.3 61.5 + - - +
702A GLY 3.3 17.3 - - - -
703A THR* 3.8 12.6 - - - -
693B LEU 4.6 1.6 + - - -
694B LYS* 3.8 13.0 - - - +
695B VAL* 3.1 33.4 + - - +
705B HIS* 5.4 0.4 - - - -
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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