Contacts of the strand formed by residues 732 - 743 (chain A) in PDB entry 4A0L
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 CYS 732 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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726A TYR* 3.7 3.9 - - - -
727A GLN* 2.9 27.9 + - - +
730A SER* 3.3 28.9 - - - +
731A GLN* 1.3 79.4 - - - +
733A PHE* 1.3 64.7 + - - +
793A ILE* 3.7 24.5 - - + -
794A ILE 3.3 16.2 - - - +
795A ASP* 4.6 2.0 - - - -
796A GLN* 4.1 4.3 - - - +
802A LEU* 5.3 2.7 - - + -
829A PHE* 3.7 24.0 - - - -
853A TYR* 4.3 4.3 - - + -
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Residues in contact with PHE 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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363A CYS* 3.8 12.3 - - - -
365A VAL* 3.7 29.2 - - + -
367A LEU* 4.2 9.2 - - + -
376A VAL* 3.7 22.7 - - + -
387A LEU* 6.1 0.2 - - + -
724A ILE* 3.8 29.6 - - + -
725A CYS 3.5 2.0 - - - +
726A TYR* 3.7 20.4 - + - -
732A CYS* 1.3 77.4 - - - +
734A GLY* 1.3 60.7 + - - +
735A VAL* 4.6 2.5 - - + -
792A LEU 3.5 0.5 - - - +
793A ILE* 3.5 5.0 - - - +
794A ILE* 2.8 46.6 + - + +
796A GLN* 4.0 19.3 - - + -
799A PHE* 3.9 33.7 - + - -
829A PHE* 4.3 3.1 - - - -
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Residues in contact with GLY 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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724A ILE* 3.3 5.5 - - - +
725A CYS 2.8 33.9 + - - -
733A PHE* 1.3 74.1 - - - +
735A VAL* 1.3 62.5 + - - +
791A LEU* 4.3 7.4 - - - -
792A LEU 3.4 7.0 - - - -
793A ILE* 4.4 0.7 - - - -
816A LEU* 3.3 8.9 - - - +
829A PHE* 3.7 22.0 - - - -
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Residues in contact with VAL 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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387A LEU* 3.3 36.8 - - + -
717A LEU* 5.0 0.2 - - + -
721A PRO* 4.1 16.2 - - + -
723A LYS 3.3 7.9 - - - +
724A ILE* 3.8 18.4 - - + -
733A PHE* 4.6 3.8 - - + -
734A GLY* 1.3 78.9 - - - +
736A LEU* 1.3 75.8 + - - +
737A SER* 3.8 1.2 + - - -
790A ASN 3.7 0.5 - - - +
791A LEU* 3.5 5.6 - - - +
792A LEU* 2.7 48.0 + - + +
794A ILE* 3.8 18.6 - - + -
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Residues in contact with LEU 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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722A ARG* 2.8 31.2 + - + -
723A LYS* 3.0 31.4 + - + +
735A VAL* 1.3 80.0 - - - +
737A SER* 1.3 59.8 + - - +
789A HIS* 6.3 0.2 - - - +
790A ASN 3.5 6.7 - - - +
791A LEU* 4.0 22.7 - - + -
807A PHE* 4.6 0.4 - - + -
813A ALA* 3.8 27.6 - - + +
815A SER 3.6 38.8 - - - +
816A LEU* 3.9 10.5 - - + +
831A VAL* 3.8 25.1 - - + -
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Residues in contact with SER 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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717A LEU* 5.7 0.9 - - - -
719A GLU* 2.7 29.5 + - - -
720A SER 3.1 17.0 - - - -
721A PRO* 4.4 2.7 - - - -
722A ARG* 4.6 3.8 - - - +
735A VAL* 4.7 0.2 - - - -
736A LEU* 1.3 76.4 - - - +
738A SER* 1.3 62.2 + - - +
789A HIS* 3.4 7.6 + - - +
790A ASN* 2.8 40.1 + - - +
792A LEU* 3.6 24.6 - - - +
813A ALA* 5.8 0.2 - - - +
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Residues in contact with SER 738 (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 GLU* 3.5 5.4 - - - +
720A SER* 3.0 40.5 + - - -
737A SER* 1.3 76.9 - - - +
739A ARG* 1.3 63.1 + - - +
787A GLU* 3.9 11.9 + - - +
788A VAL 3.2 12.1 - - - -
789A HIS* 3.6 28.3 - - - -
790A ASN* 5.2 0.7 - - - +
110B TYR* 3.6 16.8 + - - -
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Residues in contact with ARG 739 (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 TYR 5.8 0.2 - - - +
719A GLU* 3.6 20.4 + - + +
738A SER* 1.3 75.0 - - - +
740A ILE* 1.3 64.0 + - - +
741A GLU* 2.7 32.6 + - + +
751A ALA* 4.4 6.9 - - - +
753A ARG 5.7 0.2 - - - -
755A SER* 3.9 7.0 - - - +
757A SER* 2.8 38.1 + - - +
758A THR* 3.7 25.7 - - - +
787A GLU* 3.6 2.5 - - - -
788A VAL* 2.8 47.0 + - + +
790A ASN* 3.2 22.6 + - - +
806A GLN* 3.2 24.0 - - - +
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Residues in contact with ILE 740 (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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277A GLU* 5.3 5.6 - - - +
382A PHE* 3.9 34.1 - - + -
739A ARG* 1.3 77.4 - - - +
741A GLU* 1.3 72.5 + - - +
742A VAL* 5.1 4.0 - - + +
751A ALA* 4.4 1.0 - - - +
752A LEU* 4.0 39.4 + - + +
785A GLU* 3.5 46.2 - - + +
786A VAL 3.4 4.9 - - - +
787A GLU* 4.3 16.8 - - + +
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Residues in contact with GLU 741 (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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739A ARG* 2.7 42.5 + - + +
740A ILE* 1.3 80.6 - - - +
742A VAL* 1.3 62.5 + - - +
749A THR* 2.8 43.8 + - - +
750A THR 3.3 11.2 - - - +
751A ALA* 3.7 19.8 - - - +
752A LEU* 5.2 0.9 - - - +
785A GLU* 3.6 0.9 - - - -
786A VAL* 2.8 40.6 + - + +
788A VAL* 4.2 15.0 - - + +
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Residues in contact with VAL 742 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
740A ILE* 5.2 3.6 - - + -
741A GLU* 1.3 75.3 - - - +
743A GLN* 1.3 70.1 + - - +
744A ASP* 3.1 4.2 + - - +
749A THR* 3.4 4.6 - - - -
750A THR* 3.2 34.0 + - - +
751A ALA 5.8 0.9 - - - -
752A LEU* 4.3 25.4 - - + -
784A GLU 3.4 10.8 - - - +
785A GLU* 4.6 11.0 - - + -
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Residues in contact with GLN 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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742A VAL* 1.3 74.2 - - - +
744A ASP* 1.3 66.7 + - - +
745A THR* 3.8 3.5 + - - +
747A GLY 3.9 10.3 + - - +
748A GLY 3.5 9.1 + - - -
749A THR* 3.5 24.1 - - - +
784A GLU* 2.7 41.1 + - + +
786A VAL* 3.8 18.5 - - - +
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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