Contacts of the helix formed by residues 769 - 780 (chain B) in PDB entry 1LD7
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 ASN 769 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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285A GLN* 5.7 0.8 - - - +
733B GLN* 2.9 30.5 + - - +
768B LEU* 1.3 70.5 - - - +
770B LEU* 1.3 60.2 + - - +
771B LYS* 3.1 34.0 + - - +
772B SER* 3.0 33.4 + - - +
773B LEU* 3.2 7.6 + - - +
2C FRU 3.0 35.8 + - - +
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Residues in contact with LEU 770 (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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756B LEU* 4.6 11.9 - - + -
765B GLU* 3.7 26.2 - - + +
766B ARG* 5.1 1.1 - - - -
768B LEU* 3.2 18.0 + - + +
769B ASN* 1.3 71.7 + - - +
771B LYS* 1.3 57.6 + - - +
773B LEU* 3.7 5.0 - - + +
774B LEU* 2.9 31.4 + - - +
811B LEU* 4.1 22.5 - - + +
814B ALA* 4.0 19.3 - - + -
815B LEU* 4.1 23.7 - - + +
818B GLN* 3.3 30.5 - - - +
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Residues in contact with LYS 771 (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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285A GLN* 4.8 21.0 + - - +
320A GLU* 5.2 10.3 - - - +
355A TYR* 5.1 2.3 + - - +
769B ASN* 3.1 31.4 + - - +
770B LEU* 1.3 78.3 - - - +
772B SER* 1.3 74.0 + - - +
774B LEU* 3.4 7.8 + - - +
775B GLN* 3.1 30.2 + - + +
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Residues in contact with SER 772 (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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281A LYS* 6.5 1.6 - - - +
285A GLN* 4.6 10.8 - - - -
733B GLN* 3.4 2.1 + - - -
736B GLU 3.9 2.3 - - - +
737B GLY* 3.4 9.0 - - - -
769B ASN* 3.0 31.1 + - - +
771B LYS* 1.3 81.8 - - - +
773B LEU* 1.3 66.0 + - - +
775B GLN* 4.0 6.4 - - - +
776B TRP* 3.1 24.3 + - - +
2C FRU 2.9 29.3 + - - -
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Residues in contact with LEU 773 (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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733B GLN* 4.4 2.5 - - - +
737B GLY 3.2 20.9 - - - +
739B ILE* 4.4 6.1 - - + -
752B THR* 3.9 29.2 - - + -
756B LEU* 4.5 14.8 - - + -
768B LEU* 3.6 31.9 - - + -
769B ASN 3.2 16.0 + - - +
770B LEU* 3.7 7.0 - - + +
771B LYS 3.2 0.2 - - - -
772B SER* 1.3 76.2 + - - +
774B LEU* 1.3 66.7 + - - +
776B TRP* 3.2 3.2 + - + +
777B VAL* 3.0 28.2 + - + +
807B LEU* 4.7 3.8 - - + -
811B LEU* 4.1 22.2 - - + -
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Residues in contact with LEU 774 (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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355A TYR* 3.8 16.8 - - + -
358A TYR* 3.7 30.1 - - + -
359A ILE* 5.7 0.4 - - + -
770B LEU 2.9 19.2 + - - +
771B LYS* 3.7 6.5 - - - +
773B LEU* 1.3 76.7 - - - +
775B GLN* 1.3 63.4 + - - +
777B VAL* 3.3 1.2 - - - +
778B THR* 3.0 36.0 + - + +
808B LEU* 3.8 15.7 - - + -
811B LEU* 3.7 26.9 - - + +
815B LEU* 4.4 10.3 - - + -
829B MET* 3.7 28.5 - - + -
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Residues in contact with GLN 775 (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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281A LYS* 3.8 27.2 - - - +
313A ALA* 5.0 4.2 + - - +
317A ASP* 3.1 32.6 + - - +
320A GLU* 5.6 0.5 - - - +
355A TYR* 3.3 30.8 + - + +
356A TRP* 4.1 18.0 - - - -
771B LYS* 3.1 21.3 + - - +
772B SER* 4.1 6.1 - - - +
773B LEU 3.3 0.2 - - - -
774B LEU* 1.3 79.4 - - - +
776B TRP* 1.3 60.5 + - - +
778B THR* 3.1 12.7 + - - +
779B SER* 2.9 28.0 + - - +
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Residues in contact with TRP 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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278A ASN* 5.7 3.6 - - - -
736B GLU* 3.4 41.0 + - + +
738B GLY* 3.5 17.3 - - - +
747B ALA* 3.6 35.2 - - + +
748B HIS* 4.0 1.3 - - - -
749B GLY 3.5 18.6 - - - -
752B THR* 3.5 34.3 - - + -
772B SER 3.1 20.5 + - - +
773B LEU 3.2 4.7 + - - +
775B GLN* 1.3 76.8 - - - +
777B VAL* 1.3 85.4 + - + +
779B SER* 3.1 9.3 + - - -
780B ARG* 3.1 59.1 + - - +
790B GLY 4.3 1.3 - - - -
791B ARG* 4.8 0.7 - - - -
792B CYS 5.1 1.2 - - - +
804B GLN* 3.4 24.2 - - - -
807B LEU* 4.3 0.2 - - + -
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Residues in contact with VAL 777 (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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773B LEU* 3.0 18.6 + - + +
774B LEU* 3.3 11.9 - - - +
776B TRP* 1.3 91.1 - - + +
778B THR* 1.3 71.9 + - + +
780B ARG* 2.9 20.2 + - - +
788B PHE* 3.7 7.3 - - + -
804B GLN* 3.5 43.1 - - + +
807B LEU* 3.8 12.6 - - + -
808B LEU* 4.4 13.0 - - + -
811B LEU* 3.8 22.9 - - + -
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Residues in contact with THR 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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352A ARG* 2.9 37.8 + - - +
355A TYR* 4.0 22.2 - - + -
774B LEU* 3.0 34.1 + - + +
775B GLN* 3.1 13.9 + - - -
777B VAL* 1.3 76.9 - - - +
779B SER* 1.3 59.2 + - - +
780B ARG 3.4 0.7 + - - -
781B GLN* 3.5 11.3 + - - +
788B PHE* 5.1 3.6 - - - -
808B LEU* 4.0 8.1 - - + -
829B MET 3.2 27.6 - - - +
830B PHE* 5.7 2.2 - - - -
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Residues in contact with SER 779 (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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274A GLU* 3.7 24.4 + - - +
352A ARG* 3.5 24.9 + - - +
775B GLN* 2.9 20.7 + - - +
776B TRP* 3.1 13.0 + - - -
778B THR* 1.3 79.2 + - - +
780B ARG* 1.3 74.7 + - - +
781B GLN 3.2 3.5 + - - +
782B MET* 5.6 0.5 - - - +
789B GLN* 4.1 3.1 + - - -
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Residues in contact with ARG 780 (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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274A GLU* 2.7 34.6 + - - -
278A ASN* 4.9 2.4 - - - +
776B TRP* 3.1 69.8 + - + +
777B VAL* 2.9 16.6 + - - +
779B SER* 1.3 86.5 + - - +
781B GLN* 1.3 60.9 + - - +
782B MET* 3.5 1.6 + - - +
788B PHE* 3.4 5.2 - - + -
789B GLN* 2.8 75.1 + - - +
791B ARG 4.1 1.1 - - - -
792B CYS* 3.6 25.1 - - - +
804B GLN* 3.4 29.8 - - - +
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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