Contacts of the helix formed by residues 775 - 784 (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 SER 775 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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301B ANP 4.2 10.8 + - - -
773B LEU 4.4 1.4 - - - +
774B GLY* 1.3 75.1 - - - +
776B LEU* 1.3 65.0 + - - +
777B LEU* 3.8 6.7 + - - +
778B ASP* 2.9 37.5 + - - +
779B HIS* 3.3 21.4 + - - +
818B ALA 4.1 1.6 - - - -
819B ARG* 3.7 21.7 - - - +
821B VAL 3.4 11.7 - - - -
822B LEU* 3.7 9.9 - - - +
823B LEU* 4.7 1.5 - - - +
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Residues in contact with LEU 776 (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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775B SER* 1.3 70.5 - - - +
777B LEU* 1.3 65.4 + - - +
779B HIS* 3.2 6.5 + - + +
780B VAL* 3.0 32.7 + - + +
795B TRP* 3.4 41.7 - - + -
799B ILE* 4.0 5.6 - - + -
818B ALA* 3.8 6.3 - - + +
821B VAL* 2.7 45.5 + - + +
822B LEU* 4.3 0.8 - - - +
823B LEU* 4.1 16.8 - - + +
829B VAL* 4.4 1.6 - - + -
885B LEU* 3.7 38.1 - - + -
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Residues in contact with LEU 777 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
775B SER* 3.2 6.7 - - - +
776B LEU* 1.3 80.9 - - - +
778B ASP* 1.3 66.4 + - - +
780B VAL* 3.2 8.4 - - + +
781B ARG* 3.0 67.2 + - - +
818B ALA* 3.3 22.0 + - + +
819B ARG* 3.9 26.2 - - + +
858B TRP* 6.4 0.7 - - + -
884B GLU* 3.4 25.4 - - + +
889B GLY* 3.8 16.4 - - - -
890B ALA 5.6 0.2 - - - +
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Residues in contact with ASP 778 (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 5.5 3.3 + - - -
774B GLY* 6.1 0.2 - - - -
775B SER* 2.9 27.5 + - - +
776B LEU 3.5 0.2 - - - -
777B LEU* 1.3 83.6 - - - +
779B HIS* 1.3 56.5 + - - +
781B ARG* 3.5 15.0 + - - +
782B GLN* 3.0 30.1 + - - +
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Residues in contact with HIS 779 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
773B LEU* 5.1 6.4 + - + +
775B SER 3.3 12.8 + - - +
776B LEU* 3.4 10.8 - - + +
777B LEU 3.1 0.4 - - - -
778B ASP* 1.3 78.7 - - - +
780B VAL* 1.3 57.6 + - - +
782B GLN* 3.4 3.2 + - - -
783B HIS* 3.0 57.1 + + - +
787B LEU* 3.7 20.1 - - + +
795B TRP* 3.6 30.0 - + - -
823B LEU* 3.6 29.0 - - + +
826B PRO* 4.8 7.9 + - + -
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Residues in contact with VAL 780 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
776B LEU* 3.0 36.8 + - + +
777B LEU* 3.2 18.4 - - + +
779B HIS* 1.3 72.5 - - + +
781B ARG* 1.3 62.6 + - - +
784B ARG* 2.8 30.2 + - - +
787B LEU* 3.8 27.4 - - + -
792B LEU* 4.7 2.9 - - + -
795B TRP* 4.4 3.6 - - + -
818B ALA* 6.2 0.7 - - + -
884B GLU 4.5 4.0 - - - +
885B LEU* 4.7 15.5 - - + +
888B PHE* 3.8 13.9 - - + +
889B GLY* 3.6 27.1 - - - +
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Residues in contact with ARG 781 (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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777B LEU* 3.0 55.5 + - - +
778B ASP* 3.6 16.4 + - - +
780B VAL* 1.3 78.2 - - - +
782B GLN* 1.3 62.1 + - - +
784B ARG* 3.5 17.3 + - - +
888B PHE 4.1 9.4 - - - +
889B GLY* 2.2 43.5 + - - +
890B ALA 4.5 4.4 - - - -
891B GLU* 4.5 22.8 + - - +
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Residues in contact with GLN 782 (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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778B ASP 3.0 18.4 + - - +
779B HIS* 3.7 2.9 - - - +
780B VAL 3.3 0.2 - - - -
781B ARG* 1.3 79.6 - - - +
783B HIS* 1.3 82.1 + - + +
784B ARG* 4.7 1.4 - - - +
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Residues in contact with HIS 783 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
779B HIS* 3.0 38.6 + + - +
782B GLN* 1.3 103.0 - - + +
784B ARG* 1.3 72.4 + - - +
786B ALA* 3.4 26.3 + - + +
787B LEU* 4.1 20.9 - - + +
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Residues in contact with ARG 784 (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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780B VAL* 2.8 29.8 + - - +
781B ARG* 3.5 16.3 + - - +
782B GLN 4.7 1.6 - - - +
783B HIS* 1.3 75.1 - - - +
785B GLY* 1.3 65.0 + - - +
786B ALA 3.1 2.1 + - - -
787B LEU* 3.2 23.4 + - - +
887B THR 4.4 5.9 + - - -
888B PHE* 3.5 56.7 + - + +
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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