Contacts of the helix formed by residues 726 - 737 (chain D) in PDB entry 3KXX
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 726 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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724D ASN 4.3 0.2 - - - -
725D CYS* 1.3 80.4 - - - +
727D ASN* 1.3 64.0 + - - +
728D GLU* 3.4 15.6 - - - +
729D LEU* 2.9 40.6 + - + +
730D TYR* 3.4 15.6 + - - +
761D THR* 6.1 1.1 - - - +
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Residues in contact with ASN 727 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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721D LYS* 3.9 20.8 - - - +
725D CYS 4.7 0.5 - - - +
726D THR* 1.3 72.7 - - - +
728D GLU* 1.3 61.2 + - - +
730D TYR* 3.3 7.7 + - - +
731D MET* 2.9 41.2 + - + +
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Residues in contact with GLU 728 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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726D THR* 3.4 19.0 + - - +
727D ASN* 1.3 77.0 - - - +
729D LEU* 1.3 64.1 + - + +
731D MET* 3.2 10.7 + - - +
732D MET* 2.9 29.0 + - - +
756D ARG* 4.6 5.7 + - - -
757D ILE* 3.2 44.7 - - + +
760D LEU* 4.0 18.9 - - - +
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Residues in contact with LEU 729 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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601D VAL* 4.6 13.0 - - + -
690D LEU* 5.3 1.4 - - + +
694D PHE* 3.4 43.7 - - + -
725D CYS* 3.8 15.3 - - - -
726D THR* 2.9 33.8 + - + +
727D ASN 3.3 0.4 - - - -
728D GLU* 1.3 83.8 - - + +
730D TYR* 1.3 61.8 + - - +
732D MET* 3.0 36.2 + - + +
733D MET* 3.0 18.2 + - - +
754D LEU* 4.5 13.5 - - + -
757D ILE* 4.6 14.1 - - + -
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Residues in contact with TYR 730 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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691D TRP* 5.7 0.2 - + - -
719D MET 3.0 11.9 + - - -
720D ASP* 3.8 5.4 - - - -
721D LYS* 3.3 65.9 + - + -
722D PRO* 4.3 0.4 - - + -
726D THR 3.4 4.2 + - - +
727D ASN* 3.3 7.7 + - - +
729D LEU* 1.3 78.8 - - - +
731D MET* 1.3 89.2 + - + +
733D MET* 2.9 36.9 + - + +
734D ARG* 2.6 61.4 + - - +
737D TRP* 4.8 6.7 - + - -
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Residues in contact with MET 731 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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727D ASN* 2.9 29.5 + - + +
728D GLU* 3.2 12.1 + - - +
730D TYR* 1.3 112.3 - - + +
732D MET* 1.3 53.5 + - - +
734D ARG* 3.2 15.1 + - + +
735D ASP* 2.5 39.7 + - - +
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Residues in contact with MET 732 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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686D PHE* 5.3 0.9 - - - -
690D LEU* 4.2 22.0 - - + -
728D GLU 2.9 10.9 + - - +
729D LEU* 3.0 26.2 - - + +
731D MET* 1.3 74.3 - - - +
733D MET* 1.3 61.4 + - - +
735D ASP* 3.0 24.3 + - + +
736D CYS* 3.1 19.2 + - - -
745D PRO* 6.0 0.2 - - + -
750D LEU* 4.3 25.4 - - + +
753D ASP* 5.0 6.5 - - + -
754D LEU* 4.1 28.0 - - + +
757D ILE* 3.3 34.5 - - + -
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Residues in contact with MET 733 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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687D GLY* 4.2 4.0 - - - +
690D LEU* 4.1 20.4 - - + -
691D TRP* 3.8 39.0 - - - -
694D PHE* 4.1 9.6 - - + -
722D PRO* 3.8 27.1 - - + -
725D CYS* 3.8 16.2 - - - -
729D LEU 3.0 8.0 + - - +
730D TYR* 2.9 34.9 + - + +
732D MET* 1.3 77.4 - - - +
734D ARG* 1.3 61.7 + - - +
736D CYS* 3.5 6.4 + - - +
737D TRP* 3.1 49.5 + - + -
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Residues in contact with ARG 734 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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718D ARG* 3.3 29.5 + - - +
719D MET 3.2 14.1 + - - -
730D TYR* 2.6 66.1 + - + +
731D MET* 3.3 22.1 - - + +
732D MET 3.1 0.2 - - - -
733D MET* 1.3 75.1 - - - +
735D ASP* 1.3 66.9 + - - +
737D TRP* 3.2 13.2 + - - -
738D HIS* 3.2 19.1 + - - +
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Residues in contact with ASP 735 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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731D MET* 2.5 28.5 + - - +
732D MET* 3.0 20.0 - - + +
734D ARG* 1.3 77.1 - - - +
736D CYS* 1.3 62.3 + - - +
738D HIS* 3.1 23.5 - - - +
743D GLN 5.0 0.2 - - - +
744D ARG* 3.9 0.3 - - - +
745D PRO* 3.5 29.3 - - + +
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Residues in contact with CYS 736 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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683D VAL* 3.4 42.8 - - + +
684D TRP* 3.9 6.8 - - - -
686D PHE* 4.4 8.5 - - - -
687D GLY* 4.1 12.1 - - - -
690D LEU* 4.9 1.8 - - - -
732D MET* 3.1 19.2 + - - -
733D MET* 3.8 5.6 - - - +
735D ASP* 1.3 79.8 - - - +
737D TRP* 1.3 59.4 - - - +
738D HIS 3.0 0.4 + - - -
744D ARG* 3.0 28.9 + - - -
745D PRO* 4.1 3.8 - - - -
750D LEU* 3.9 25.8 - - - -
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Residues in contact with TRP 737 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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684D TRP* 3.2 46.3 + + + -
687D GLY* 3.3 24.5 - - - -
688D VAL* 3.2 24.1 - - + +
691D TRP* 3.8 16.6 - + + -
701D TYR* 5.4 4.0 - - - -
718D ARG* 2.8 57.5 + - + +
719D MET* 3.5 52.3 - - + -
730D TYR* 4.8 3.1 - + - -
733D MET* 3.1 36.5 + - + +
734D ARG* 3.2 14.3 + - - +
736D CYS* 1.3 74.2 - - - +
738D HIS* 1.3 59.5 + - - +
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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