Contacts of the helix formed by residues 833 - 841 (chain B) in PDB entry 1L8A
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 833 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101A LEU* 4.0 38.4 - - - +
103A LEU* 4.0 4.7 - - - +
167A GLN* 4.3 0.9 + - - -
634B ASN* 3.8 7.9 - - - +
832B ASP* 1.3 85.1 + - - +
834B ARG* 1.3 67.7 + - - +
835B GLU* 3.9 7.8 + - - +
836B ASN* 3.2 29.6 + - - +
837B LEU* 3.0 21.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 834 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101A LEU 4.9 1.2 + - - +
102A GLU* 2.9 45.6 + - + +
631B THR 3.6 14.6 - - - +
632B THR* 2.9 21.2 + - - +
634B ASN* 3.4 22.8 + - - +
693B ASN* 3.0 33.1 + - - +
694B GLU* 3.4 37.6 - - - +
833B SER* 1.3 73.2 - - - +
835B GLU* 1.3 58.5 + - - +
837B LEU* 3.7 0.5 - - - +
838B ARG* 2.9 57.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 835 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101A LEU* 6.5 0.2 - - + -
833B SER* 4.0 8.5 - - - +
834B ARG* 1.3 81.5 - - - +
836B ASN* 1.3 67.0 + - - +
838B ARG* 3.3 6.2 + - - +
839B HIS* 3.1 23.6 + - + +
844B ASP* 4.7 2.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 836 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167A GLN* 3.7 6.8 - - - +
169A VAL* 4.1 8.2 - - + +
170A HIS* 3.3 34.3 + - - -
832B ASP* 2.8 36.4 - - - +
833B SER* 3.2 13.3 + - - +
835B GLU* 1.3 86.8 + - - +
837B LEU* 1.3 58.3 + - - +
839B HIS* 3.4 7.3 + - - +
840B HIS* 2.9 29.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 837 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169A VAL* 3.7 22.4 - - + -
631B THR* 3.8 23.1 - - + +
634B ASN* 3.5 28.3 - - + +
641B GLU* 3.5 28.9 - - - +
830B ARG* 3.5 23.1 - - + +
832B ASP* 3.9 8.1 - - + -
833B SER 3.0 16.8 + - - +
834B ARG 3.7 3.4 - - - +
836B ASN* 1.3 78.0 - - - +
838B ARG* 1.3 59.2 + - - +
840B HIS* 4.3 1.3 - - + -
841B PHE* 2.8 46.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 838 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
631B THR* 2.9 29.7 + - + +
632B THR* 3.1 23.0 + - - +
694B GLU* 2.8 42.6 + - - -
733B SER* 3.7 7.2 + - - -
734B ILE* 3.9 15.6 - - + +
736B ARG* 3.8 2.2 - - - +
737B HIS* 3.2 34.5 + - + -
834B ARG* 2.9 42.7 + - - +
835B GLU* 3.3 6.0 + - - +
837B LEU* 1.3 75.8 - - - +
839B HIS* 1.3 58.4 + - - +
841B PHE 4.1 0.4 - - - -
842B GLU 3.5 0.5 + - - -
843B VAL* 3.0 32.2 + - + -
844B ASP* 3.1 24.4 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 839 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
835B GLU* 3.1 16.0 + - + +
836B ASN* 3.7 8.5 - - - +
838B ARG* 1.3 77.4 - - - +
840B HIS* 1.3 65.4 + - - +
841B PHE 3.3 0.2 - - - -
842B GLU* 3.0 10.0 + - - +
844B ASP* 2.6 23.4 + - - +
846B SER* 3.5 19.3 - - - -
847B TYR* 3.3 34.7 + + - -
874B PHE 3.6 14.3 + - - -
875B ASN* 3.1 23.8 + - - +
876B ILE* 4.0 4.8 - - + -
877B ASP 5.9 0.4 - - - -
880B LYS* 4.3 4.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 840 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169A VAL* 3.8 36.9 - - + +
830B ARG* 3.8 31.1 + - - -
836B ASN 2.9 18.8 + - - +
837B LEU* 3.7 3.8 - - - +
839B HIS* 1.3 78.4 - - - +
841B PHE* 1.3 77.8 + + - +
842B GLU 3.3 2.1 + - - -
880B LYS* 3.1 45.2 + - + +
881B VAL* 5.8 0.4 - - - +
883B PRO* 3.2 24.3 - - + +
886B ALA* 3.8 20.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 841 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
630B ARG* 3.6 22.2 - - + -
631B THR* 3.9 15.5 - - + -
641B GLU* 4.4 8.7 - - - -
824B GLY 3.0 19.6 - - - +
825B THR* 3.4 34.8 - - + -
826B ASP 3.3 26.7 - - - -
827B GLY* 3.9 6.3 - - - -
828B PHE 3.3 24.9 - - - -
829B GLY* 4.0 2.9 - - - -
830B ARG* 4.8 1.3 - - + -
837B LEU* 2.8 36.9 + - + +
840B HIS* 1.3 94.4 - + - +
842B GLU* 1.3 69.8 + - - +
843B VAL* 3.3 5.0 + - + +
883B PRO* 4.0 11.0 - - + +
----------------------------------------------------------
Back to top of page
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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
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