Contacts of the helix formed by residues 712 - 733 (chain A) in PDB entry 1MQB
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 SER 712 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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711A PHE* 1.3 76.4 - - - +
713A VAL* 1.3 63.9 + - - +
714A LEU* 3.5 9.9 + - - +
715A GLN* 2.9 38.3 + - - +
716A LEU* 3.1 21.9 + - - +
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Residues in contact with VAL 713 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
711A PHE 3.9 1.3 + - - +
712A SER* 1.3 72.0 - - - +
714A LEU* 1.3 56.7 + - - +
716A LEU* 3.6 11.5 + - + +
717A VAL* 3.0 31.0 + - + +
811A MET* 4.7 7.9 - - + -
841A ASP* 4.4 18.2 - - + +
843A PRO* 3.4 31.9 - - + -
881A LEU* 4.0 20.4 - - + +
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Residues in contact with LEU 714 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
712A SER* 3.1 9.8 - - - +
713A VAL* 1.3 77.6 - - - +
715A GLN* 1.3 59.7 + - + +
717A VAL* 3.4 1.7 + - - +
718A GLY* 2.9 26.2 + - - -
875A ILE* 4.1 30.9 - - + +
878A PRO* 4.0 29.6 - - + -
881A LEU* 3.9 22.9 - - + +
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Residues in contact with GLN 715 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
710A GLU 4.6 1.4 - - - +
711A PHE* 3.5 24.5 - - + -
712A SER* 2.9 45.9 + - - +
714A LEU* 1.3 74.7 - - - +
716A LEU* 1.3 62.1 + - - +
718A GLY* 3.9 2.0 - - - -
719A MET* 3.1 30.2 + - + +
751A LEU* 3.6 29.3 - - + +
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Residues in contact with LEU 716 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
704A LEU* 4.3 10.3 - - + -
711A PHE* 4.1 15.3 - - + +
712A SER 3.1 16.3 + - - +
713A VAL* 3.8 14.1 - - + +
715A GLN* 1.3 77.5 - - - +
717A VAL* 1.3 57.6 + - - +
719A MET* 3.2 20.0 + - - +
720A LEU* 3.1 29.8 + - - +
810A VAL* 3.7 32.6 - - + +
811A MET* 4.0 29.6 - - + +
813A TYR* 3.8 32.3 - - + +
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Residues in contact with VAL 717 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
713A VAL* 3.0 24.0 + - + +
714A LEU* 3.9 5.4 - - - +
716A LEU* 1.3 74.0 - - - +
718A GLY* 1.3 61.3 + - - +
720A LEU* 3.1 9.5 + - + +
721A ARG* 2.9 25.3 + - - +
811A MET* 4.9 7.9 - - - -
846A ILE* 3.9 36.6 - - + -
871A LEU* 4.3 14.9 - - + +
874A LEU* 4.7 7.2 - - + -
875A ILE* 3.8 21.8 - - + -
881A LEU* 4.3 12.8 - - + -
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Residues in contact with GLY 718 (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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714A LEU 2.9 17.3 + - - -
715A GLN* 3.9 2.5 - - - -
717A VAL* 1.3 75.3 - - - +
719A MET* 1.3 62.4 + - - +
721A ARG* 3.4 5.1 + - - +
722A GLY* 3.1 19.1 + - - -
875A ILE* 4.0 16.1 - - - +
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Residues in contact with MET 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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700A LEU* 4.3 10.8 - - + -
703A PHE* 4.6 7.0 - - + -
704A LEU* 4.2 10.8 - - + -
711A PHE* 4.0 35.7 - - + -
715A GLN 3.1 23.3 + - - +
716A LEU* 3.2 24.8 + - - +
718A GLY* 1.3 74.6 - - - +
720A LEU* 1.3 58.6 + - - +
722A GLY* 3.3 2.6 + - - -
723A ILE* 3.1 34.1 + - + +
747A VAL* 5.1 1.6 - - + -
751A LEU* 3.7 36.3 - - + +
753A CYS* 3.5 26.7 - - - +
810A VAL* 4.8 6.3 - - + -
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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
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716A LEU 3.1 16.8 + - - +
717A VAL* 3.1 12.1 + - - +
719A MET* 1.3 75.6 - - - +
721A ARG* 1.3 60.2 + - - +
723A ILE* 3.6 12.1 + - + -
724A ALA* 2.9 28.1 + - - +
803A PHE* 3.5 12.2 - - + -
806A VAL* 4.2 5.2 - - + +
807A MET* 3.9 41.5 - - + -
810A VAL* 3.5 29.8 - - + -
811A MET* 4.2 21.5 - - + -
846A ILE* 4.7 11.7 - - + -
871A LEU* 3.9 11.9 - - + -
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Residues in contact with ARG 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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674A ASN* 5.5 3.4 - - - +
717A VAL 2.9 14.6 + - - +
718A GLY* 3.4 6.5 + - - +
719A MET 3.3 0.2 - - - -
720A LEU* 1.3 73.6 - - - +
722A GLY* 1.3 69.3 + - - +
724A ALA* 3.6 1.7 - - - +
725A ALA* 2.8 42.9 + - - +
868A VAL* 3.2 30.8 - - - +
871A LEU* 3.8 25.1 - - + +
872A ASP* 3.2 32.3 + - - -
875A ILE* 3.9 13.5 - - + -
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Residues in contact with GLY 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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674A ASN* 3.2 35.2 - - - +
718A GLY 3.1 14.9 + - - -
719A MET 3.3 3.5 + - - -
721A ARG* 1.3 81.1 - - - +
723A ILE* 1.3 64.9 + - - +
725A ALA* 3.2 1.0 + - - +
726A GLY 3.1 15.4 + - - -
753A CYS* 4.0 5.2 - - - -
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Residues in contact with ILE 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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674A ASN* 5.1 0.7 - - - -
700A LEU* 3.9 28.3 - - + -
719A MET 3.1 18.1 + - - +
720A LEU* 3.8 16.4 - - + +
722A GLY* 1.3 76.0 - - - +
724A ALA* 1.3 56.8 + - - +
726A GLY* 3.1 2.4 + - - -
727A MET* 2.9 26.9 + - + +
740A LEU* 4.3 12.1 - - + -
745A ILE* 4.0 27.4 - - + -
753A CYS* 3.7 18.7 + - + -
755A VAL* 4.1 8.1 - - + +
803A PHE* 3.8 20.2 - - + -
806A VAL* 4.0 17.7 - - + -
810A VAL* 4.8 0.7 - - + -
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Residues in contact with ALA 724 (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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720A LEU 2.9 19.7 + - - +
721A ARG* 3.6 7.6 - - - +
722A GLY 3.2 0.2 - - - -
723A ILE* 1.3 75.7 - - - +
725A ALA* 1.3 53.1 + - - +
727A MET* 3.1 9.2 + - - +
728A LYS* 2.7 34.1 + - - +
803A PHE* 3.8 10.1 - - + -
864A PHE* 4.1 5.2 - - + -
867A ILE* 3.8 29.2 - - + -
868A VAL* 3.6 12.4 - - + +
871A LEU* 4.1 1.1 - - + -
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Residues in contact with ALA 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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672A HIS* 4.0 11.8 + - + +
674A ASN* 3.5 17.5 - - - +
721A ARG* 2.8 41.4 + - - +
722A GLY 3.3 5.2 - - - +
724A ALA* 1.3 72.3 - - - +
726A GLY* 1.3 55.5 + - - +
728A LYS* 2.8 21.9 + - - +
729A TYR* 2.8 14.4 + - - +
868A VAL* 3.5 11.5 - - + +
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Residues in contact with GLY 726 (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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672A HIS* 4.1 7.6 - - - -
674A ASN* 3.8 25.7 - - - +
675A ILE* 3.6 11.5 - - - +
722A GLY 3.1 7.7 + - - -
723A ILE 3.5 3.6 - - - -
725A ALA* 1.3 77.4 - - - +
727A MET* 1.3 58.3 + - - +
729A TYR* 3.3 4.4 + - - +
730A LEU* 2.9 30.6 + - - +
755A VAL* 4.6 2.0 - - - -
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Residues in contact with MET 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 ILE* 2.9 19.1 + - + +
724A ALA* 3.5 3.4 - - - +
726A GLY* 1.3 78.4 - - - +
728A LYS* 1.3 56.1 + - - +
730A LEU* 3.8 24.6 - - + +
731A ALA* 3.0 29.2 + - + +
735A TYR 5.4 0.4 - - - +
737A HIS* 3.7 15.3 - - + +
740A LEU* 4.0 27.6 - - + -
755A VAL* 4.0 15.3 - - + -
799A ASP* 3.3 41.5 - - + +
864A PHE* 3.3 39.7 - - + -
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Residues in contact with LYS 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 ALA 2.7 16.0 + - - +
725A ALA* 2.8 12.9 + - - +
727A MET* 1.3 68.8 - - - +
729A TYR* 1.3 66.9 + - - +
731A ALA* 3.9 2.3 - - - +
732A ASN* 3.0 51.9 + - - +
864A PHE* 3.8 15.0 - - + +
865A ALA* 3.5 40.4 - - + +
868A VAL* 4.3 15.5 - - + -
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Residues in contact with TYR 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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669A GLN 4.0 5.2 + - - -
670A PHE* 3.4 35.8 - + + -
671A SER* 2.9 37.7 + - - -
672A HIS* 3.5 42.4 - + + +
675A ILE* 4.1 8.5 - - + -
725A ALA 2.8 8.0 + - - +
726A GLY 3.4 7.2 - - - +
728A LYS* 1.3 74.7 - - - +
730A LEU* 1.3 71.7 + - + +
732A ASN* 3.2 8.5 + - + +
733A MET* 3.1 43.7 + - + +
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Residues in contact with LEU 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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670A PHE* 3.7 39.7 - - + -
675A ILE* 3.7 18.2 - - + -
726A GLY 2.9 18.5 + - - +
727A MET* 3.8 32.3 - - + +
729A TYR* 1.3 79.6 - - + +
731A ALA* 1.3 61.6 + - - +
733A MET* 3.1 12.0 + - - +
735A TYR* 2.9 47.9 + - + +
737A HIS* 4.2 8.3 - - + -
755A VAL* 4.3 5.4 - - + -
758A PHE* 3.9 19.5 - - + -
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Residues in contact with ALA 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 MET* 3.0 19.9 + - + +
728A LYS* 4.0 4.9 - - - +
729A TYR 3.2 0.2 - - - -
730A LEU* 1.3 77.1 - - - +
732A ASN* 1.3 63.9 + - - +
734A ASN* 3.2 16.1 + - - -
735A TYR 4.2 4.9 - - - +
796A SER* 3.3 32.5 + - - +
864A PHE* 4.3 12.1 - - + +
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Residues in contact with ASN 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 LYS* 3.0 52.9 + - - +
729A TYR* 3.6 7.5 - - + +
731A ALA* 1.3 75.8 - - - +
733A MET* 1.3 57.1 + - + +
734A ASN* 3.0 17.8 + - - +
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Residues in contact with MET 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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669A GLN* 4.1 25.6 - - + +
670A PHE* 4.3 19.3 - - + -
729A TYR* 3.1 45.2 + - + +
730A LEU 3.1 7.4 + - - +
732A ASN* 1.3 73.0 - - + +
734A ASN* 1.3 71.1 + - - +
735A TYR* 3.1 3.5 + - - +
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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