Contacts of the helix formed by residues 740 - 755 (chain B) in PDB entry 2XWU
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 GLN 740 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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699B ALA* 3.5 22.6 + - - +
702B VAL* 4.4 3.9 - - - +
703B GLU* 2.8 43.4 + - - +
706B CYS* 5.5 0.2 - - - +
735B TYR* 3.4 11.5 - - - -
738B ILE* 3.5 40.3 + - + +
739B PRO* 1.3 81.9 - - - +
741B ALA* 1.3 67.9 + - - +
742B SER* 3.6 11.1 + - - +
743B ALA* 3.0 22.1 + - + +
744B LEU* 3.6 2.8 + - - +
789B ILE* 4.0 7.8 - - - +
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Residues in contact with ALA 741 (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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703B GLU* 5.4 0.4 + - - -
740B GLN* 1.3 72.4 - - - +
742B SER* 1.3 65.3 - - - +
744B LEU* 2.8 25.6 + - - +
745B ASP* 2.9 16.6 + - - +
788B ASP* 3.7 33.1 + - + +
789B ILE* 3.7 9.6 - - + +
792B SER* 3.5 19.7 + - - +
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Residues in contact with SER 742 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
703B GLU* 3.4 34.4 + - - +
706B CYS* 3.4 22.9 - - - -
710B GLU* 6.2 0.4 - - - -
740B GLN* 3.6 8.2 + - - +
741B ALA* 1.3 78.0 - - - +
743B ALA* 1.3 57.7 + - - +
745B ASP* 3.3 13.1 + - - +
746B LEU* 3.0 26.9 + - - +
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Residues in contact with ALA 743 (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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706B CYS* 4.1 6.3 - - - -
731B LEU* 3.7 28.3 - - + +
734B MET* 6.0 1.3 - - + -
735B TYR* 3.7 24.9 - - + +
738B ILE 6.0 0.2 - - - +
740B GLN* 3.0 15.4 + - + +
742B SER* 1.3 77.5 + - - +
744B LEU* 1.3 65.2 + - - +
746B LEU* 3.3 3.2 + - - +
747B THR* 2.9 28.8 + - - -
771B VAL* 5.8 1.6 - - + -
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Residues in contact with LEU 744 (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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735B TYR* 3.7 16.8 - - + +
741B ALA* 2.8 14.7 + - - +
743B ALA* 1.3 73.1 - - - +
745B ASP* 1.3 64.8 + - - +
747B THR* 3.0 8.2 + - - -
748B ARG* 2.9 24.9 + - - +
771B VAL* 2.9 38.4 - - + -
775B THR* 3.9 4.0 - - - +
789B ILE* 3.5 45.8 - - + +
792B SER* 3.8 21.5 - - - +
793B PHE* 3.9 13.0 - - + +
796B LEU* 4.2 15.4 - - + +
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Residues in contact with ASP 745 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
741B ALA* 2.9 20.7 + - - +
742B SER* 3.5 12.2 - - - +
744B LEU* 1.3 76.7 - - - +
746B LEU* 1.3 55.7 - - - +
748B ARG* 2.8 40.8 + - - +
749B GLN* 3.0 24.9 + - - +
792B SER* 3.2 24.3 + - - -
795B GLN* 3.9 1.9 - - - +
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Residues in contact with LEU 746 (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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706B CYS* 4.1 19.1 - - - +
709B PHE* 3.8 32.8 - - + +
710B GLU* 4.0 24.7 - - + +
713B VAL* 4.1 19.7 - - + -
727B LEU* 4.4 4.9 - - + -
731B LEU* 3.8 25.8 - - + -
742B SER 3.0 13.5 + - - +
743B ALA* 3.8 8.5 - - - +
745B ASP* 1.3 74.1 - - - +
747B THR* 1.3 60.0 + - - +
749B GLN* 3.1 11.3 + - + +
750B LEU* 2.9 32.9 + - + +
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Residues in contact with THR 747 (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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731B LEU* 4.3 3.1 - - - +
743B ALA 2.9 18.5 + - - -
744B LEU* 3.0 11.9 + - - -
746B LEU* 1.3 77.1 - - - +
748B ARG* 1.3 58.7 + - - +
750B LEU* 3.2 12.5 + - - +
751B VAL* 3.0 33.4 + - + +
764B ILE* 5.3 2.2 - - + -
767B LEU* 3.7 32.1 - - + +
768B PHE* 4.6 11.7 - - + +
771B VAL* 4.2 9.9 - - + +
796B LEU* 3.8 23.1 - - + -
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Residues in contact with ARG 748 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
744B LEU 2.9 11.8 + - - +
745B ASP* 2.8 44.0 + - - +
747B THR* 1.3 74.8 - - - +
749B GLN* 1.3 66.6 + - - +
751B VAL* 3.5 3.8 + - - +
752B HIS* 3.1 23.5 + - + +
792B SER 4.8 1.0 + - - -
795B GLN* 3.0 55.7 + - - +
796B LEU* 3.4 20.0 - - + +
799B GLN* 3.9 19.8 - - + +
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Residues in contact with GLN 749 (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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713B VAL* 4.3 11.7 - - + -
714B LYS* 6.0 7.4 - - + -
745B ASP 3.0 13.2 + - - +
746B LEU* 3.1 23.3 + - + +
748B ARG* 1.3 80.4 - - - +
750B LEU* 1.3 57.4 + - - +
752B HIS* 3.7 4.2 - - - +
753B ILE* 3.0 38.6 + - + +
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Residues in contact with LEU 750 (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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713B VAL* 4.0 24.2 - - + -
720B PHE* 4.7 3.4 - - + -
724B VAL* 4.9 3.4 - - + -
727B LEU* 4.0 22.9 - - + -
728B CYS* 4.4 13.2 - - - -
731B LEU* 4.5 5.8 - - + -
746B LEU* 2.9 20.0 + - + +
747B THR* 3.4 7.9 - - - +
749B GLN* 1.3 75.1 - - - +
751B VAL* 1.3 57.5 + - - +
753B ILE* 3.1 1.7 + - - -
754B PHE* 2.8 63.1 + - + -
764B ILE* 3.7 16.6 - - + +
767B LEU* 4.2 23.8 - - + -
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Residues in contact with VAL 751 (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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747B THR* 3.0 25.1 + - + +
748B ARG* 3.8 5.8 - - - +
750B LEU* 1.3 73.8 - - - +
752B HIS* 1.3 58.6 + - - +
755B ALA* 2.8 42.8 + - + +
761B PHE* 4.9 8.1 - - + -
764B ILE* 3.8 23.8 - - + -
768B PHE* 4.9 11.7 - - + -
796B LEU* 4.2 14.8 - - + -
799B GLN* 4.2 16.4 - - + +
800B ALA* 4.3 18.6 - - + +
803B ARG* 5.0 1.1 - - + -
804B LYS* 4.9 10.3 - - + -
807B LEU* 4.9 2.7 - - + -
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Residues in contact with HIS 752 (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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748B ARG* 3.1 14.0 + - + +
749B GLN* 3.7 5.8 - - - +
751B VAL* 1.3 81.0 - - - +
753B ILE* 1.3 73.2 + - + +
755B ALA* 3.9 9.6 + - - +
756B HIS* 4.8 4.0 + - - -
799B GLN* 2.9 30.9 + - - +
803B ARG* 4.9 13.2 + - + +
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Residues in contact with ILE 753 (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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713B VAL* 3.4 40.8 - - + +
714B LYS* 5.6 0.4 - - - -
717B LEU* 3.9 23.6 - - + +
718B ASP* 3.3 24.2 - - - +
749B GLN* 3.0 22.8 + - + +
750B LEU 3.7 2.2 - - - +
752B HIS* 1.3 87.9 - - + +
754B PHE* 1.3 89.6 + - + +
756B HIS* 3.2 24.1 - - - -
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Residues in contact with PHE 754 (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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713B VAL* 5.6 0.4 - - + -
717B LEU 3.5 13.2 - - - -
718B ASP* 3.8 22.9 - - + -
720B PHE* 4.4 4.3 - + + -
721B ALA* 3.9 15.5 - - + -
724B VAL* 3.4 26.9 - - + -
750B LEU* 2.8 37.6 + - + -
751B VAL 3.8 2.2 - - - -
753B ILE* 1.3 97.0 - - + +
755B ALA* 1.3 62.3 + - - +
756B HIS* 3.3 4.6 + + - -
757B GLU* 3.5 20.4 - - + +
760B HIS* 4.7 15.0 - + + -
761B PHE* 3.5 22.3 - - - +
764B ILE* 3.4 27.6 - - + -
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Residues in contact with ALA 755 (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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751B VAL* 2.8 23.4 + - + +
752B HIS 3.9 6.5 + - - +
753B ILE 3.5 2.4 - - - -
754B PHE* 1.3 79.9 - - - +
756B HIS* 1.3 61.7 + - - +
757B GLU 4.9 1.6 - - - -
758B PRO* 5.6 1.9 - - - +
761B PHE* 4.3 12.5 - - - -
803B ARG* 3.7 39.3 - - + +
804B LYS* 4.9 5.5 - - + +
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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