Contacts of the helix formed by residues 718 - 733 (chain A) in PDB entry 2Y4Q
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 718 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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714A GLY* 4.2 27.1 - - - +
717A LEU* 1.3 77.5 - - - +
719A LYS* 1.3 73.0 + - + +
720A ASN* 4.1 15.5 - - + +
721A THR* 2.9 37.8 + - - +
722A VAL* 3.5 4.5 + - - +
782A LEU* 3.6 6.2 - - - +
786A ARG* 5.1 13.0 - - - +
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Residues in contact with LYS 719 (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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718A LYS* 1.3 80.7 - - + +
720A ASN* 1.3 64.9 + - + +
722A VAL* 3.5 5.3 + - - +
723A ASP* 3.3 22.0 + - - +
782A LEU* 3.4 31.4 - - + +
786A ARG* 3.5 35.3 - - - +
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Residues in contact with ASN 720 (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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718A LYS* 3.0 13.6 - - + -
719A LYS* 1.3 83.5 - - + +
721A THR* 1.3 64.7 + - - +
723A ASP* 3.3 16.2 + - - +
724A ASP* 2.9 31.4 + - - +
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Residues in contact with THR 721 (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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717A LEU* 6.4 0.4 - - - -
718A LYS* 2.9 29.6 + - - +
720A ASN* 1.3 77.6 - - - +
722A VAL* 1.3 64.6 + - - +
724A ASP* 2.9 19.8 + - - +
725A ILE* 3.0 18.6 + - + +
745A LEU* 6.4 0.2 - - + -
750A HIS* 5.1 9.9 - - + +
754A GLU* 3.6 21.7 + - - +
758A ILE* 3.0 37.2 - - + -
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Residues in contact with VAL 722 (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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717A LEU* 5.5 1.1 - - + -
718A LYS 3.6 4.0 - - - +
719A LYS* 3.8 6.3 - - - +
720A ASN 3.4 0.4 - - - -
721A THR* 1.3 75.0 - - - +
723A ASP* 1.3 52.8 + - - +
725A ILE* 4.0 0.4 - - - -
726A SER* 2.6 40.2 + - - -
775A HIS* 3.7 15.5 - - + -
778A MET* 3.2 44.9 - - + +
779A ARG* 4.2 17.0 - - + -
782A LEU* 3.0 37.5 - - + -
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Residues in contact with ASP 723 (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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719A LYS 3.3 11.5 + - - +
720A ASN* 3.4 14.1 - - - +
721A THR 3.1 0.8 - - - -
722A VAL* 1.3 77.7 - - - +
724A ASP* 1.3 62.5 + - - +
726A SER* 3.8 6.1 - - - -
727A GLU* 3.1 35.3 + - - +
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Residues in contact with ASP 724 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
720A ASN* 2.9 34.2 + - - +
721A THR* 2.9 6.4 + - - +
723A ASP* 1.3 78.3 - - - +
725A ILE* 1.3 58.9 + - - +
727A GLU* 2.8 33.7 - - - +
728A SER* 3.3 10.6 + - - -
745A LEU* 4.5 4.6 - - + +
748A LYS* 4.5 10.8 - - - +
750A HIS* 3.0 45.6 + - + +
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Residues in contact with ILE 725 (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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721A THR* 3.0 23.9 + - + +
722A VAL 3.9 1.8 - - - +
724A ASP* 1.3 73.7 - - - +
726A SER* 1.3 60.7 + - - +
728A SER* 3.5 5.0 + - - -
729A LEU* 2.9 29.1 + - + +
741A LEU* 3.9 26.0 - - + +
745A LEU* 4.3 22.4 - - + -
758A ILE* 3.6 37.9 - - + -
759A PHE* 5.6 0.7 - - + -
770A LEU* 4.4 5.8 - - + -
775A HIS* 3.7 18.6 - - + +
778A MET* 3.6 23.1 - - + -
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Residues in contact with SER 726 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
722A VAL* 2.6 25.9 + - - -
723A ASP* 3.8 6.7 - - - -
725A ILE* 1.3 73.2 - - - +
727A GLU* 1.3 62.7 + - - +
729A LEU* 3.2 3.8 + - - +
730A ARG* 3.0 23.7 + - - +
775A HIS* 3.0 28.4 + - - -
779A ARG* 5.2 5.6 + - - -
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Residues in contact with GLU 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 ASP* 3.1 25.8 + - - +
724A ASP* 2.8 41.1 - - - +
726A SER* 1.3 76.1 - - - +
728A SER* 1.3 66.4 + - - +
730A ARG* 3.2 7.2 + - - +
731A GLN* 2.8 38.5 + - - +
748A LYS* 3.3 28.1 + - - +
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Residues in contact with SER 728 (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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724A ASP 3.3 13.2 + - - -
725A ILE* 3.9 5.2 - - - -
726A SER 3.3 0.4 - - - -
727A GLU* 1.3 82.1 - - - +
729A LEU* 1.3 60.6 + - - +
731A GLN* 3.4 7.6 + - - +
732A GLY 3.3 15.4 + - - -
736A LEU* 3.6 7.6 - - - +
741A LEU* 3.5 17.7 + - - +
744A ASP* 3.0 42.3 + - - +
745A LEU* 5.5 2.9 - - - -
748A LYS* 4.2 11.4 - - - +
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Residues in contact with LEU 729 (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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725A ILE* 2.9 18.6 + - + +
726A SER* 3.5 7.6 - - - +
727A GLU 3.2 0.2 - - - -
728A SER* 1.3 75.6 - - - +
730A ARG* 1.3 58.1 + - - +
732A GLY 3.3 1.7 + - - -
733A GLY 3.2 5.5 + - - -
734A GLY* 2.8 59.7 + - - +
736A LEU* 3.3 15.0 - - + +
741A LEU* 3.5 33.8 - - + +
770A LEU* 4.4 15.5 - - + +
771A THR* 4.1 2.2 - - - -
772A GLU* 4.0 16.6 - - + +
775A HIS* 4.0 30.3 - - + -
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Residues in contact with ARG 730 (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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726A SER 3.0 13.2 + - - +
727A GLU* 3.2 10.5 + - - +
729A LEU* 1.3 77.3 - - - +
731A GLN* 1.3 79.2 + - - +
733A GLY* 3.4 10.9 + - - -
734A GLY* 4.3 5.2 - - - +
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Residues in contact with GLN 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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727A GLU* 2.8 38.2 + - - +
728A SER* 3.6 12.4 - - - +
729A LEU 3.2 0.4 - - - -
730A ARG* 1.3 105.3 + - - +
732A GLY* 1.3 59.5 + - - +
733A GLY 3.6 0.2 + - - -
744A ASP* 5.0 7.9 - - - +
748A LYS* 5.3 4.9 - - - +
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Residues in contact with GLY 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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728A SER 3.3 4.4 + - - -
729A LEU 3.3 3.8 + - - -
730A ARG 3.3 0.6 - - - -
731A GLN* 1.3 78.9 - - - +
733A GLY* 1.3 58.3 + - - +
734A GLY 3.8 0.4 - - - -
735A LYS* 3.5 17.1 - - - +
736A LEU* 3.4 26.0 - - - +
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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 LEU 3.2 1.2 + - - -
730A ARG 3.4 7.5 + - - -
731A GLN 3.3 3.8 + - - -
732A GLY* 1.3 80.8 - - - +
734A GLY* 1.3 60.0 + - - +
735A LYS* 3.0 20.9 + - - +
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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