Contacts of the helix formed by residues 737 - 754 (chain A) in PDB entry 1N54
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 THR 737 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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724A HIS* 3.3 19.1 - - + -
728A CYS* 4.9 1.1 - - - -
734A SER* 3.4 24.0 - - - +
735A VAL 2.6 10.2 + - - +
736A LEU* 1.3 75.6 - - - +
738A PRO* 1.3 75.1 - - + +
739A TRP* 4.1 6.9 - - - +
740A TYR* 2.8 36.0 + - - +
741A LYS* 2.8 12.9 + - - +
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Residues in contact with PRO 738 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
440A ASP* 5.5 2.2 - - - +
442A GLU* 3.4 50.3 - - + +
443A SER* 4.9 7.9 - - - +
444A PRO* 5.6 3.8 - - + -
736A LEU 4.3 2.9 - - - +
737A THR* 1.3 87.6 - - + +
739A TRP* 1.3 53.3 + - - +
741A LYS* 3.5 10.0 - - + +
742A ASN* 2.5 37.1 + - - -
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Residues in contact with TRP 739 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
442A GLU* 5.2 10.0 + - - +
629A SER* 4.7 6.3 + - - +
632A PHE* 4.0 38.1 - + + +
633A THR* 3.8 19.5 - - + +
720A ILE* 3.3 34.8 - - + -
721A LEU* 5.4 0.9 - - + -
724A HIS* 4.1 29.8 - + + -
727A ARG* 6.0 5.2 - - - -
737A THR* 3.0 6.0 - - - +
738A PRO* 1.3 77.6 - - - +
740A TYR* 1.3 70.8 + + - +
742A ASN* 3.7 7.0 + - - +
743A CYS* 3.0 41.4 + - + +
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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
----------------------------------------------------------
721A LEU* 4.3 17.9 - - + -
724A HIS* 3.8 20.9 - + + +
725A LEU* 4.3 11.9 - - + -
735A VAL* 3.3 35.2 - - + +
736A LEU* 4.4 19.1 - - + -
737A THR* 2.8 24.4 + - - +
739A TRP* 1.3 80.8 - + - +
741A LYS* 1.3 74.7 + - - +
743A CYS* 4.4 1.3 - - - -
744A ILE* 2.9 55.4 + - + +
777A HIS* 3.3 35.2 + + - +
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Residues in contact with LYS 741 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218A THR* 5.8 1.4 + - - +
402A LEU 5.5 0.4 - - - -
403A ASP 4.2 17.8 + - - +
404A THR* 4.4 5.1 + - - +
405A MET 2.9 28.8 + - - -
407A THR* 4.2 5.2 - - - +
410A VAL* 6.0 1.6 - - - -
444A PRO* 4.9 15.0 - - + -
736A LEU* 6.1 3.6 - - + -
737A THR 2.8 10.5 + - - +
738A PRO* 3.5 14.4 - - + +
739A TRP 3.3 0.2 - - - -
740A TYR* 1.3 84.0 - - - +
742A ASN* 1.3 72.6 + - - +
744A ILE* 3.0 7.6 - - - +
745A GLU* 2.9 53.6 + - - +
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Residues in contact with ASN 742 (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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407A THR* 3.9 26.1 + - + +
442A GLU 5.2 3.4 + - - -
447A LYS* 4.7 17.7 - - - +
632A PHE 5.9 0.2 - - - +
633A THR* 3.4 39.6 - - + +
638A TRP* 6.1 1.1 - - + +
738A PRO* 2.5 27.2 + - - +
739A TRP 4.0 0.4 - - - +
740A TYR 3.4 0.2 - - - -
741A LYS* 1.3 87.7 - - - +
743A CYS* 1.3 65.8 + - - +
745A GLU* 3.7 0.5 - - - +
746A ARG* 2.8 36.7 + - + +
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Residues in contact with CYS 743 (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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632A PHE* 4.3 10.7 - - + -
633A THR* 5.3 0.8 - - - +
638A TRP* 5.4 1.1 - - - -
717A PHE* 3.3 18.7 - - - -
720A ILE* 3.4 33.4 - - - -
721A LEU* 3.5 23.1 - - + -
739A TRP* 3.0 45.2 + - + +
740A TYR* 4.0 2.0 - - - +
742A ASN* 1.3 74.0 - - - +
744A ILE* 1.3 62.9 + - - +
746A ARG* 3.3 5.5 + - - +
747A LEU* 3.2 16.6 + - - +
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Residues in contact with ILE 744 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
721A LEU* 4.0 18.1 - - + +
740A TYR* 2.9 64.1 + - + +
741A LYS* 3.0 8.7 - - - +
743A CYS* 1.3 75.1 - - - +
745A GLU* 1.3 74.2 + - + +
747A LEU* 3.4 28.6 + - + +
748A GLN* 3.3 15.9 + - - +
777A HIS 4.2 18.4 - - - +
778A ILE* 4.5 7.0 - - + -
781A VAL* 4.7 11.8 - - + +
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Residues in contact with GLU 745 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218A THR* 5.2 8.8 - - - +
406A ASN* 3.4 31.0 + - - +
407A THR* 2.3 42.8 + - - +
408A THR* 4.8 1.7 + - - +
741A LYS* 2.9 48.3 + - + +
742A ASN 3.9 0.2 - - - +
744A ILE* 1.3 86.0 - - + +
746A ARG* 1.3 54.5 + - - +
748A GLN* 2.8 19.8 + - - +
749A GLN* 2.7 32.4 + - - +
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Residues in contact with ARG 746 (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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407A THR* 3.7 23.6 - - + +
411A ASP* 3.3 20.4 + - - -
633A THR 4.3 7.9 + - - -
635A LEU* 3.6 29.5 - - - +
638A TRP* 3.2 64.2 - - + +
642A HIS* 5.2 0.2 - - - -
717A PHE* 3.8 14.8 - - + -
742A ASN* 2.8 33.2 + - + +
743A CYS 3.5 4.9 - - - +
745A GLU* 1.3 76.2 - - - +
747A LEU* 1.3 59.3 + - - +
749A GLN* 2.8 47.6 + - - +
750A ILE* 3.1 16.6 + - - +
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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
----------------------------------------------------------
714A PHE* 3.6 32.1 - - + +
717A PHE* 3.5 33.1 - - + -
718A ILE* 5.8 1.8 - - + -
721A LEU* 3.5 27.8 - - + -
743A CYS 3.2 8.4 + - - +
744A ILE* 3.4 21.3 - - + +
746A ARG* 1.3 78.6 - - - +
748A GLN* 1.3 59.0 + - - +
750A ILE* 3.6 4.7 + - - +
751A PHE* 3.5 25.7 + - + -
770A PHE* 4.5 7.0 - - + -
778A ILE* 4.5 13.0 - - + -
781A VAL* 4.4 15.0 - - + -
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Residues in contact with GLN 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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212A PRO 4.4 3.1 - - - +
213A MET* 3.9 37.5 + - + +
362A LEU* 4.9 0.6 - - - +
406A ASN* 2.7 38.2 + - - +
408A THR* 4.1 4.9 + - - -
744A ILE 3.3 4.1 + - - +
745A GLU* 2.8 24.4 + - - +
747A LEU* 1.3 76.8 - - - +
749A GLN* 1.3 56.6 + - - +
750A ILE 3.1 1.8 - - - -
751A PHE* 3.0 5.5 + - - +
752A LEU* 2.8 55.2 + - + +
781A VAL* 4.1 21.8 - - + +
784A GLN* 4.6 2.9 - - - +
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Residues in contact with GLN 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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408A THR* 3.7 38.5 + - + +
411A ASP* 3.9 11.5 + - - +
638A TRP* 4.8 0.2 - - - +
642A HIS* 3.5 21.6 + - - +
745A GLU 2.7 14.1 + - - +
746A ARG* 2.8 49.1 + - - +
748A GLN* 1.3 73.1 - - - +
750A ILE* 1.3 56.8 + - + +
752A LEU* 3.6 7.4 - - + -
753A GLN* 3.0 55.7 + - + +
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Residues in contact with ILE 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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638A TRP* 5.2 4.7 - - + -
641A LEU* 5.2 7.0 - - + -
642A HIS* 3.5 31.0 - - + +
645A ILE* 5.0 7.0 - - + -
710A PHE* 4.4 19.7 - - + -
713A ILE* 4.6 16.2 - - + -
714A PHE* 4.3 21.3 - - + -
717A PHE* 4.0 21.3 - - + -
746A ARG 3.1 16.8 + - - +
747A LEU* 3.6 9.0 - - - +
748A GLN 3.1 0.4 - - - -
749A GLN* 1.3 78.5 - - + +
751A PHE* 1.3 63.2 + - - +
754A HIS* 3.2 27.1 + - + +
758A ILE* 3.6 7.6 - - - +
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Residues in contact with PHE 751 (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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213A MET* 4.5 5.8 - - + -
714A PHE* 3.4 30.3 - + - -
747A LEU* 3.5 14.1 + - + -
748A GLN* 3.0 9.1 + - - +
750A ILE* 1.3 81.2 - - - +
752A LEU* 1.3 57.3 + - - +
755A HIS* 3.1 29.3 - - - +
758A ILE* 4.0 11.9 - - + -
765A LEU* 4.3 5.6 - - + -
770A PHE* 3.6 32.3 - + - -
781A VAL* 3.1 35.9 - - + -
782A PHE* 3.8 31.2 - + - -
785A PHE* 3.8 33.7 - + + -
788A LEU* 5.1 0.3 - - - +
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Residues in contact with LEU 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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213A MET* 3.1 48.0 - - + +
214A LEU* 4.8 6.7 - - + -
362A LEU* 4.2 20.0 - - + -
363A PRO* 3.4 30.0 - - + +
364A ALA* 5.9 0.2 - - - +
408A THR* 4.7 4.7 - - + +
748A GLN* 2.8 43.2 + - + +
749A GLN* 3.9 7.9 - - + +
750A ILE 3.1 0.2 - - - -
751A PHE* 1.3 78.9 - - - +
753A GLN* 1.3 62.9 + - + +
755A HIS* 2.9 25.8 - - - -
788A LEU* 4.7 8.1 - - + -
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Residues in contact with GLN 753 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363A PRO* 5.4 3.1 - - - +
364A ALA* 6.0 8.5 - - + -
408A THR* 5.0 6.5 - - + +
412A ARG* 5.5 5.2 - - - +
642A HIS* 3.6 29.3 + - - +
646A ARG* 5.2 4.5 + - - +
749A GLN* 3.0 45.7 + - + +
752A LEU* 1.3 79.2 - - + +
754A HIS* 1.3 82.2 + - + +
755A HIS* 3.4 5.6 + - - -
756A GLN* 5.2 1.2 + - - +
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Residues in contact with HIS 754 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
642A HIS* 3.8 21.3 + + + -
645A ILE* 3.4 33.3 - - + +
646A ARG* 4.6 15.7 - - + -
649A ASN* 3.1 25.5 + - - +
710A PHE* 3.7 26.9 - + + -
750A ILE* 3.2 17.3 + - + +
753A GLN* 1.3 95.9 + - + +
755A HIS* 1.3 66.3 + - - +
756A GLN* 3.3 3.4 - - - -
757A ILE* 3.2 15.3 + - + +
758A ILE* 3.2 16.6 + - + +
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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