Contacts of the strand formed by residues 774 - 784 (chain E) in PDB entry 2X36
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 GLY 774 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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770E TRP* 3.6 10.0 - - - -
771E THR* 2.6 45.1 + - - +
773E MET* 1.3 80.1 - - - +
775E GLY* 1.3 54.1 + - - -
897E GLU* 3.9 15.9 - - - -
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Residues in contact with GLY 775 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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769E ALA 3.5 6.7 - - - -
771E THR* 4.2 2.7 + - - +
774E GLY* 1.3 73.6 - - - -
776E SER* 1.3 61.9 + - - -
897E GLU* 3.5 28.8 - - - +
900E ILE* 6.3 0.2 - - - -
901E ALA* 4.0 9.3 - - - +
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Residues in contact with SER 776 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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768E LEU* 3.5 3.5 - - - -
769E ALA* 2.6 46.8 + - - +
771E THR* 3.4 22.2 - - - +
775E GLY* 1.3 77.2 - - - -
777E THR* 1.3 70.0 + - - +
778E LEU* 3.3 18.3 - - - +
901E ALA* 3.8 10.9 - - - +
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Residues in contact with THR 777 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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766E MET* 3.1 34.3 - - + -
767E GLY 3.5 4.3 - - - -
768E LEU* 3.3 21.8 - - - +
776E SER* 1.3 78.7 + - - +
778E LEU* 1.3 70.1 + - - +
779E PHE* 4.6 13.9 - - + -
901E ALA* 3.7 15.9 + - - +
905E ALA* 3.9 12.0 - - + +
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Residues in contact with LEU 778 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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766E MET* 4.5 1.1 - - - -
767E GLY* 2.7 44.1 + - - +
769E ALA* 3.5 28.0 - - + -
776E SER* 3.3 23.1 - - - +
777E THR* 1.3 76.4 - - - +
779E PHE* 1.3 64.5 + - - +
780E VAL* 3.4 5.4 + - + +
844E VAL* 6.1 1.6 - - + -
845E PRO* 3.9 31.9 - - + +
846E GLU 3.7 27.4 - - - +
847E GLY* 5.0 1.1 - - - -
848E ALA* 4.9 4.5 - - + +
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Residues in contact with PHE 779 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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758E ASP* 4.1 29.2 - - - -
760E THR* 3.9 23.6 - - + -
764E VAL* 3.5 25.4 - - + -
765E VAL 3.5 6.3 - - - +
766E MET* 4.5 21.8 - - + +
777E THR* 4.6 16.2 - - + -
778E LEU* 1.3 73.4 - - - +
780E VAL* 1.3 62.1 + - - +
781E GLU* 3.8 8.7 + - + +
843E HIS* 5.0 0.7 + - - -
845E PRO* 3.1 24.9 - - - +
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Residues in contact with VAL 780 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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763E GLY 3.8 0.8 - - - +
764E VAL* 3.3 6.6 - - - +
765E VAL 2.7 31.3 + - - +
767E GLY* 4.8 1.8 - - - +
778E LEU* 3.4 7.6 + - + +
779E PHE* 1.3 73.9 - - - +
781E GLU* 1.3 62.4 + - - +
782E THR 4.4 0.2 - - - -
842E LEU* 3.5 26.0 - - + -
843E HIS 3.6 5.6 - - - +
844E VAL* 4.2 16.8 - - + -
845E PRO* 4.5 1.1 - - + -
856E ALA* 5.3 4.9 - - + -
859E THR* 3.3 32.5 - - + +
860E ILE* 4.1 22.9 - - + -
863E ALA* 4.3 8.4 - - + +
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Residues in contact with GLU 781 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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763E GLY 3.5 1.1 - - - -
764E VAL* 3.3 28.2 - - + +
779E PHE* 4.6 8.9 - - + +
780E VAL* 1.3 73.6 - - - +
782E THR* 1.3 66.2 - - - +
783E SER* 4.2 3.4 + - - -
841E HIS* 3.3 4.7 + - - +
842E LEU* 3.5 1.3 - - - -
843E HIS* 2.8 60.0 + - + +
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Residues in contact with THR 782 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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762E PRO 4.5 2.6 - - - +
763E GLY* 2.7 26.8 + - - +
764E VAL* 5.5 0.7 - - - +
780E VAL 4.4 0.2 - - - -
781E GLU* 1.3 78.5 - - - +
783E SER* 1.3 60.5 + - - +
840E ILE* 4.2 5.6 - - + -
841E HIS 3.5 4.9 - - - +
842E LEU* 4.0 16.4 - - + -
860E ILE 4.8 0.2 - - - +
863E ALA* 2.9 39.9 + - + -
864E LEU* 3.5 29.4 - - + -
867E LEU* 3.3 23.3 - - - +
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Residues in contact with SER 783 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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781E GLU* 4.2 4.9 + - - -
782E THR* 1.3 75.6 - - - +
784E LEU* 1.3 73.0 + - - +
840E ILE* 3.4 5.9 - - - +
841E HIS* 3.0 47.8 + - - +
867E LEU* 3.9 9.4 - - - -
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Residues in contact with LEU 784 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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783E SER* 1.3 85.8 + - - +
785E ARG* 1.3 63.1 + - - +
834E TYR* 3.3 29.3 + - + +
838E SER* 3.5 28.7 - - - -
839E HIS 3.7 9.0 - - - +
840E ILE* 4.8 1.3 - - + +
867E LEU* 4.0 7.5 - - + +
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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