Contacts of the helix formed by residues 719 - 737 (chain A) in PDB entry 4KSC
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 719 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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715A ILE 2.9 12.5 + - - -
716A ILE* 4.1 3.1 - - - -
718A GLY* 1.3 71.8 - - - +
720A LEU* 1.3 62.2 + - - +
722A PRO* 3.2 10.5 - - - +
723A ALA* 4.0 8.3 + - - +
836A ILE* 4.6 3.9 - - - +
837A ALA* 4.2 1.8 - - - +
841A THR* 3.2 30.1 - - - +
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Residues in contact with LEU 720 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
716A ILE 3.3 16.2 + - - +
717A ASN* 3.2 20.6 - - - +
718A GLY 3.0 0.4 - - - -
719A GLY* 1.3 77.9 - - - +
721A GLN* 1.3 65.4 + - - +
723A ALA* 3.2 22.0 + - + +
724A PHE 3.7 2.8 + - - -
757A ILE* 3.3 41.5 - - + +
758A LEU* 4.0 12.0 - - + +
761A ILE* 3.6 30.3 - - + -
762A SER* 3.7 25.4 - - - +
765A THR* 4.5 2.2 - - + -
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Residues in contact with GLN 721 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303A TYR* 4.4 17.9 + - - -
717A ASN 3.4 5.9 + - - +
718A GLY* 3.2 9.5 + - - +
720A LEU* 1.3 79.5 - - - +
722A PRO* 1.4 68.4 - - + +
723A ALA 3.3 0.5 + - - -
724A PHE* 3.4 28.7 + - - +
725A SER* 3.7 5.4 + - - -
758A LEU* 5.2 5.9 - - - +
833A PHE* 5.5 4.7 - - + -
837A ALA* 4.5 4.3 - - + -
978A VAL* 4.7 21.0 + - - +
979A PHE* 4.5 6.3 - - + -
982A MET* 3.6 34.8 - - + +
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Residues in contact with PRO 722 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
718A GLY 3.1 15.3 - - - +
719A GLY 3.2 10.3 - - - +
721A GLN* 1.4 89.0 - - + +
723A ALA* 1.3 51.8 + - - +
725A SER* 2.9 5.4 + - - -
726A VAL* 2.6 44.1 + - + +
837A ALA 3.1 23.6 - - - +
841A THR* 3.6 28.3 - - + -
845A ILE* 5.2 2.2 - - + -
979A PHE* 3.3 30.9 - - + -
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Residues in contact with ALA 723 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
719A GLY 4.0 6.3 + - - +
720A LEU* 3.2 18.0 + - + +
722A PRO* 1.3 78.3 - - - +
724A PHE* 1.3 52.6 + - - +
726A VAL* 3.0 10.3 + - - +
727A ILE* 2.5 45.9 + - + +
757A ILE* 4.0 21.5 - - + -
841A THR* 5.6 0.2 - - - +
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Residues in contact with PHE 724 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303A TYR* 3.9 26.0 - + + -
306A TYR* 3.5 44.2 - + - -
720A LEU 3.7 1.8 + - - -
721A GLN* 3.4 21.2 + - - +
722A PRO 3.2 0.2 - - - -
723A ALA* 1.3 78.5 - - - +
725A SER* 1.3 80.8 + - - +
727A ILE* 3.8 7.9 - - - +
728A PHE* 3.0 34.0 + + + +
754A LEU* 4.1 13.0 - - + -
757A ILE* 5.3 0.2 - - - +
758A LEU* 3.5 41.1 - - + +
978A VAL* 6.0 4.7 - - + -
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Residues in contact with SER 725 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
721A GLN* 3.9 4.0 + - - -
722A PRO 2.9 10.1 + - - -
724A PHE* 1.3 92.6 - - - +
726A VAL* 1.3 56.2 + - - +
728A PHE* 4.6 7.0 - - - +
729A SER* 3.1 21.0 + - - -
971A LEU 4.8 0.2 - - - +
974A PHE* 6.4 1.3 - - - -
975A SER* 3.1 40.0 + - - -
978A VAL* 3.5 22.7 - - - +
979A PHE* 3.6 9.9 - - - -
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Residues in contact with VAL 726 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
722A PRO* 2.6 24.7 + - + +
723A ALA* 3.3 11.4 - - - +
725A SER* 1.3 73.8 - - - +
727A ILE* 1.3 69.2 + - + +
729A SER* 3.2 7.1 + - - -
730A LYS* 3.0 25.1 + - + +
841A THR* 6.3 0.4 - - + -
845A ILE* 3.7 35.7 - - + -
972A LEU* 5.8 5.4 - - + -
975A SER* 4.8 4.3 - - - +
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Residues in contact with ILE 727 (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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723A ALA* 2.5 26.5 + - + +
724A PHE* 3.8 6.7 - - - +
726A VAL* 1.3 75.3 - - + +
728A PHE* 1.3 64.0 + - - +
730A LYS* 3.0 9.0 + - - +
731A VAL* 3.0 29.2 + - + +
750A LEU* 3.6 29.0 - - + +
753A LEU* 3.3 50.5 - - + +
754A LEU* 3.6 21.3 - - + -
757A ILE* 4.0 17.9 - - + -
758A LEU* 6.0 0.4 - - + -
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Residues in contact with PHE 728 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306A TYR* 3.5 16.8 - - - +
310A PHE* 3.4 41.1 - + - -
329A THR* 5.7 10.1 - - + -
724A PHE* 3.0 24.5 + + + +
725A SER* 4.6 5.8 - - - +
727A ILE* 1.3 77.5 - - - +
729A SER* 1.3 66.4 + - - +
731A VAL* 3.3 19.1 + - + +
732A VAL* 3.3 45.7 + - + +
754A LEU* 4.3 11.9 - - + +
971A LEU* 5.1 10.1 - - + -
974A PHE* 5.3 17.3 - + - -
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Residues in contact with SER 729 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
725A SER 3.1 21.0 + - - -
726A VAL* 3.2 8.7 + - - -
727A ILE 3.2 0.2 - - - -
728A PHE* 1.3 82.2 - - - +
730A LYS* 1.3 57.1 + - - +
732A VAL* 3.9 3.0 - - - +
733A GLY* 3.0 26.3 + - - -
967A PHE* 5.4 2.1 + - - +
968A GLU* 5.7 0.5 - - - -
971A LEU* 3.2 40.3 - - - +
972A LEU* 3.4 20.7 - - - +
975A SER* 4.6 0.2 - - - -
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Residues in contact with LYS 730 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
726A VAL* 3.0 15.5 + - + +
727A ILE* 3.0 9.8 + - - +
729A SER* 1.3 75.8 + - - +
731A VAL* 1.3 60.3 + - - +
733A GLY* 4.3 1.6 - - - +
734A VAL* 2.9 35.7 + - + +
746A GLN* 4.6 13.6 + - - -
750A LEU* 3.6 32.0 - - + +
967A PHE* 5.6 11.2 - - + -
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Residues in contact with VAL 731 (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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310A PHE* 5.8 7.6 - - + -
314A THR* 5.4 9.6 - - + -
727A ILE* 3.0 28.1 + - + +
728A PHE* 3.3 14.8 + - + +
730A LYS* 1.3 76.3 - - - +
732A VAL* 1.3 66.4 + - + +
734A VAL* 3.4 5.0 - - - +
735A PHE* 3.0 30.9 + - + +
747A ASN* 3.8 21.2 + - + +
750A LEU* 3.7 32.5 - - + -
751A PHE* 5.0 2.2 - - - +
754A LEU* 5.3 4.3 - - + -
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Residues in contact with VAL 732 (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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310A PHE* 5.9 1.1 - - + -
329A THR* 5.6 5.8 - - - +
728A PHE* 3.4 44.2 - - + +
729A SER* 3.9 5.4 - - - +
731A VAL* 1.3 83.3 - - + +
733A GLY* 1.3 55.2 + - - +
735A PHE* 3.6 8.7 - - + -
736A THR* 2.5 48.1 + - + +
971A LEU* 4.2 22.2 - - + -
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Residues in contact with GLY 733 (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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729A SER 3.0 22.9 + - - -
730A LYS 3.8 0.7 - - - -
731A VAL 3.1 0.2 - - - -
732A VAL* 1.3 78.3 - - - +
734A VAL* 1.3 51.3 + - - +
736A THR* 2.6 19.3 + - - -
737A ASN 2.7 20.4 + - - +
967A PHE* 3.5 31.0 - - - +
971A LEU* 4.9 3.6 - - - -
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Residues in contact with VAL 734 (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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86A LYS* 6.0 3.8 - - - -
730A LYS* 2.9 25.9 + - + +
731A VAL* 3.4 7.2 - - - +
733A GLY* 1.3 74.2 - - - +
735A PHE* 1.3 64.8 + - - +
737A ASN 2.9 25.5 - - - +
738A GLY* 3.4 13.1 - - - -
743A THR* 5.5 3.5 - - - +
746A GLN* 4.2 34.5 - - + +
747A ASN* 4.2 13.2 - - - +
750A LEU* 4.8 4.3 - - + -
967A PHE* 4.5 8.7 - - + -
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Residues in contact with PHE 735 (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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79A ALA* 4.9 4.5 - - + +
83A ASN* 4.3 12.8 + - - -
314A THR* 4.6 16.4 - - + -
317A VAL* 3.4 42.8 - - + -
318A ILE* 4.6 10.8 - - + -
324A ILE* 4.6 15.5 - - + -
325A GLY* 6.0 1.1 - - - -
328A LEU* 6.1 1.3 - - + -
731A VAL* 3.0 19.2 + - + +
732A VAL* 3.4 12.3 - - + +
733A GLY 3.1 0.2 - - - -
734A VAL* 1.3 79.6 - - - +
736A THR* 1.3 66.2 + - + +
738A GLY 4.6 1.2 - - - +
743A THR* 5.5 13.9 - - + +
747A ASN* 3.1 37.5 - - - -
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Residues in contact with THR 736 (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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75A THR* 4.2 25.4 - - + -
78A PHE* 4.1 25.8 - - + -
79A ALA* 3.3 35.7 - - + +
82A GLY* 3.3 8.1 - - - -
83A ASN* 4.0 0.5 + - - -
732A VAL* 2.5 36.3 + - + +
733A GLY* 2.6 18.7 + - - -
735A PHE* 1.3 77.5 - - + +
737A ASN* 1.3 56.7 + - - -
738A GLY 3.6 1.4 + - - +
967A PHE* 4.4 4.5 - - - +
971A LEU* 5.5 5.0 - - + +
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Residues in contact with ASN 737 (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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78A PHE* 5.2 9.8 - - + -
82A GLY* 3.8 16.2 - - - +
85A SER* 4.1 15.4 + - - -
86A LYS* 4.6 9.9 + - - +
733A GLY 2.7 8.7 + - - -
734A VAL* 2.9 26.2 - - - +
736A THR* 1.3 71.6 + - - +
738A GLY* 1.3 61.4 + - - +
965A MET 4.5 10.9 + - - -
966A THR* 4.8 1.2 - - - +
967A PHE* 3.5 47.2 - - + +
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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