Contacts of the helix formed by residues 739 - 760 (chain A) in PDB entry 1U1H
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 LYS 739 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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441A PRO* 3.9 4.7 - - + -
738A ARG* 1.3 76.6 - - - +
740A TYR* 1.3 70.4 + - + +
741A THR* 3.1 46.0 - - - +
742A GLU* 2.6 43.9 + - - +
743A VAL* 3.1 8.3 + - - +
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Residues in contact with TYR 740 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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440A PHE* 3.6 27.0 - + - +
441A PRO* 3.0 44.5 + - + +
443A THR* 3.4 24.2 - - + -
469A GLU* 3.6 3.1 + - - -
473A LYS* 3.2 29.4 - - + +
476A ASP* 4.5 16.6 - - + -
739A LYS* 1.3 85.8 - - + +
741A THR* 1.3 56.8 + - + +
742A GLU 3.0 0.2 - - - -
743A VAL* 3.2 17.5 - - + -
744A LYS* 3.0 49.6 + - + +
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Residues in contact with THR 741 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
705A ILE* 4.0 3.3 - - - +
739A LYS* 2.8 41.9 + - - +
740A TYR* 1.3 76.4 - - + +
742A GLU* 1.3 64.1 + - - +
744A LYS* 5.3 0.9 - - - -
745A PRO* 3.4 20.3 - - - +
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Residues in contact with GLU 742 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
698A TYR* 3.4 4.7 + - - +
703A PRO* 3.3 38.2 - - - +
704A ARG 5.8 0.2 - - - -
705A ILE* 3.1 22.6 - - + +
738A ARG* 2.8 42.9 + - + +
739A LYS* 2.6 29.6 + - - +
741A THR* 1.3 83.2 + - - +
743A VAL* 1.3 57.5 + - - +
744A LYS 3.6 0.2 - - - -
745A PRO* 4.1 0.7 - - - -
746A ALA* 2.9 25.3 + - - +
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Residues in contact with VAL 743 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
440A PHE* 5.1 2.0 - - + -
441A PRO* 3.7 15.0 - - + -
698A TYR* 3.8 8.1 - - - +
735A LEU* 3.9 26.5 - - + -
738A ARG* 3.5 33.7 - - + -
739A LYS 3.1 0.6 + - - +
740A TYR* 3.2 40.8 - - + -
742A GLU* 1.3 76.3 - - - +
744A LYS* 1.3 62.3 + - + +
746A ALA* 4.1 0.4 - - - -
747A LEU* 2.7 44.6 + - + +
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Residues in contact with LYS 744 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
476A ASP* 3.5 27.1 + - - +
479A GLU* 5.2 7.4 + - - -
480A GLU* 3.1 26.5 - - - +
740A TYR* 3.0 28.1 + - + +
741A THR* 5.3 0.7 - - - -
743A VAL* 1.3 89.0 - - + +
745A PRO* 1.3 71.8 - - + +
747A LEU* 3.9 1.7 - - - +
748A LYS* 3.1 17.3 + - - +
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Residues in contact with PRO 745 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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705A ILE* 3.9 21.1 - - + -
741A THR* 3.4 25.4 - - - +
742A GLU 4.0 2.0 - - - +
743A VAL 3.9 0.7 - - - -
744A LYS* 1.3 96.1 - - + +
746A ALA* 1.3 58.2 + - - +
748A LYS* 3.4 14.0 + - + +
749A ASN* 2.6 38.2 + - - +
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Residues in contact with ALA 746 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
698A TYR* 3.4 35.8 - - + -
705A ILE* 3.4 15.0 - - + +
706A PRO* 4.0 4.7 - - + -
711A ILE* 4.1 4.9 - - - +
742A GLU 2.9 21.3 - - - +
743A VAL 3.5 3.1 - - - +
744A LYS 3.2 0.8 - - - -
745A PRO* 1.3 81.6 - - - +
747A LEU* 1.3 64.0 + - - +
749A ASN* 3.1 16.5 + - - +
750A MSE 3.2 11.7 + - - +
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Residues in contact with LEU 747 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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436A THR* 4.3 11.2 - - + -
440A PHE* 4.1 21.1 - - + -
480A GLU* 4.3 11.4 - - + -
481A LEU* 3.0 24.5 - - + +
483A ILE* 4.8 3.8 - - + -
698A TYR* 4.8 7.2 - - + -
731A PRO* 4.1 25.8 - - + -
735A LEU* 3.9 24.7 - - + -
743A VAL* 2.7 28.6 + - + +
744A LYS* 3.9 3.1 - - - +
746A ALA* 1.3 73.6 - - + +
748A LYS* 1.3 63.2 + - - +
750A MSE 2.9 31.4 + - + +
751A VAL 3.1 6.9 + - - -
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Residues in contact with LYS 748 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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480A GLU* 3.7 17.8 + - - +
481A LEU* 3.4 12.2 - - + +
744A LYS* 3.1 24.7 + - - +
745A PRO* 3.7 13.8 - - - +
746A ALA 3.3 0.2 - - - -
747A LEU* 1.3 77.1 - - - +
749A ASN* 1.3 60.3 + - - +
751A VAL* 2.7 24.0 - - + +
752A ASP* 3.1 26.7 - - - +
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Residues in contact with ASN 749 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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705A ILE* 3.6 8.3 - - - +
706A PRO 2.8 25.5 + - - +
707A SER* 3.9 3.5 - - - +
708A SER* 3.1 41.4 + - - +
711A ILE* 3.9 4.0 - - + -
745A PRO* 2.6 26.0 + - - +
746A ALA* 3.1 5.8 + - - +
748A LYS* 1.3 79.2 - - - +
750A MSE 1.3 66.2 + - - +
752A ASP* 4.9 1.7 - - - +
753A ALA* 3.0 24.4 + - - +
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Residues in contact with MSE 750 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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434A THR* 4.2 16.6 - - + -
435A THR 3.7 15.9 - - - +
436A THR* 5.1 1.1 - - + -
481A LEU* 4.8 7.9 - - + -
483A ILE* 5.6 1.6 - - + -
697A VAL* 3.9 13.2 - - + -
698A TYR* 5.2 4.3 - - + -
711A ILE* 3.5 17.9 - - + +
729A VAL* 3.4 40.5 - - + +
730A ASN* 3.6 26.9 - - - -
731A PRO* 3.9 13.0 - - + -
746A ALA 3.2 6.2 + - - +
747A LEU* 2.9 27.0 + - + +
749A ASN* 1.3 78.3 - - - +
751A VAL* 1.3 60.7 + - - +
753A ALA* 3.3 5.2 - - - +
754A ALA* 3.1 20.8 + - - +
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Residues in contact with VAL 751 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
434A THR* 4.5 10.8 - - + +
481A LEU* 2.8 65.9 - - + +
747A LEU 3.1 1.4 + - - -
748A LYS* 2.7 29.8 - - + +
750A MSE 1.3 78.8 - - - +
752A ASP* 1.3 73.5 + - - +
754A ALA* 3.1 5.1 + - - +
755A LYS* 2.8 50.1 + - + +
758A ARG* 6.1 1.3 - - - +
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Residues in contact with ASP 752 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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708A SER* 3.8 17.2 + - - +
748A LYS* 3.1 31.0 + - - +
749A ASN* 3.8 6.0 - - - +
751A VAL* 1.3 89.5 - - - +
753A ALA* 1.3 57.6 + - - +
755A LYS* 3.8 10.8 - - - +
756A LEU* 2.8 33.8 + - - +
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Residues in contact with ALA 753 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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708A SER* 3.7 6.7 - - - +
711A ILE* 3.6 9.0 - - + -
712A ALA* 3.3 41.3 - - + +
715A VAL* 5.4 2.7 - - + -
749A ASN 3.0 13.8 + - - +
750A MSE 3.3 10.3 - - - +
752A ASP* 1.3 78.4 - - - +
754A ALA* 1.3 56.9 + - - +
756A LEU* 3.4 4.6 - - - +
757A ILE* 2.9 36.4 + - - +
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Residues in contact with ALA 754 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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432A LEU* 4.1 18.6 - - + +
434A THR* 4.1 22.4 - - + -
715A VAL* 5.9 2.0 - - - -
729A VAL* 4.3 13.8 - - + +
750A MSE 3.1 9.8 + - - +
751A VAL* 3.1 7.7 + - + +
753A ALA* 1.3 76.1 - - - +
755A LYS* 1.3 68.7 + - + +
757A ILE* 2.9 9.8 + - - +
758A ARG* 2.7 31.6 + - - +
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Residues in contact with LYS 755 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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481A LEU* 4.3 2.5 + - - +
482A ASP* 3.0 29.0 + - - -
751A VAL* 2.8 44.0 + - + +
752A ASP* 3.8 10.8 - - - +
754A ALA* 1.3 72.4 - - - +
756A LEU* 1.3 64.4 + - - +
758A ARG* 3.0 44.4 - - - +
759A SER* 3.1 7.4 + - - -
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Residues in contact with LEU 756 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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712A ALA* 4.7 15.5 - - + -
752A ASP 2.8 19.7 + - - +
753A ALA* 3.4 5.4 - - - +
754A ALA 2.9 0.2 + - - -
755A LYS* 1.3 75.3 - - - +
757A ILE* 1.3 58.6 + - + +
759A SER* 2.5 39.6 + - - +
760A GLN* 3.2 34.0 + - - +
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Residues in contact with ILE 757 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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432A LEU* 3.6 23.8 - - + -
712A ALA* 3.9 17.9 - - + +
715A VAL* 4.4 10.8 - - + -
716A ASN* 3.1 38.4 - - - +
719A LEU* 3.7 21.5 - - + -
753A ALA 2.9 28.0 + - - +
754A ALA 2.9 9.1 + - - +
756A LEU* 1.3 75.3 - - + +
758A ARG* 1.3 62.2 + - - +
760A GLN* 3.3 33.2 + - + +
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Residues in contact with ARG 758 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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430A PRO* 3.5 25.9 - - - +
431A ILE* 2.9 37.8 + - + +
432A LEU* 2.9 28.3 + - + -
433A PRO 4.1 0.6 - - - -
434A THR* 4.1 7.1 - - - +
484A ASP* 2.7 33.9 + - - -
751A VAL* 6.1 1.0 - - - +
754A ALA* 2.7 18.3 + - - +
755A LYS* 3.0 40.7 - - - +
756A LEU 2.8 1.0 + - - -
757A ILE* 1.3 75.5 - - - +
759A SER* 1.3 62.7 + - - +
760A GLN 4.1 3.6 - - - -
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Residues in contact with SER 759 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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755A LYS 3.1 5.9 + - - -
756A LEU* 2.5 33.8 + - - +
758A ARG* 1.3 74.0 - - - +
760A GLN* 1.3 78.8 + - - +
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Residues in contact with GLN 760 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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756A LEU* 3.2 44.1 + - - +
757A ILE* 3.6 28.6 - - + +
758A ARG 3.3 3.5 - - - -
759A SER* 1.3 108.2 + - - +
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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
------------------------------------------------------------
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) + - + + + + + -
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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