Contacts of the helix formed by residues 700 - 718 (chain A) in PDB entry 3APO
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 700 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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697A ALA* 2.9 20.2 + - - -
698A PRO 3.1 0.6 - - - -
699A TRP* 1.3 98.4 - - - +
701A GLY* 1.3 64.1 + - - +
702A PRO* 3.6 7.1 - - - +
703A SER* 2.9 27.1 + - - -
704A GLN* 2.9 26.2 + - - +
743A TYR* 3.6 16.7 + - - -
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Residues in contact with GLY 701 (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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699A TRP 3.5 5.9 + - - -
700A SER* 1.3 68.3 - - - +
702A PRO* 1.4 66.0 - - - +
704A GLN* 3.0 16.3 + - - +
705A ASN* 2.8 40.3 + - - -
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Residues in contact with PRO 702 (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 SER* 3.6 9.2 - - - +
701A GLY* 1.4 90.0 - - - +
703A SER* 1.3 58.5 + - - +
705A ASN* 3.9 10.9 - - + +
706A PHE* 3.3 24.3 + - - +
743A TYR 4.2 4.5 - - - +
744A PRO* 3.6 19.3 - - + +
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Residues in contact with SER 703 (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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694A ASP* 5.3 2.1 - - - +
696A TYR* 3.6 19.4 - - - +
697A ALA 3.3 27.0 + - - -
700A SER* 2.9 32.5 + - - -
702A PRO* 1.3 73.4 - - - +
704A GLN* 1.3 64.5 + - - +
706A PHE* 3.3 3.6 + - - +
707A ALA* 3.1 23.7 + - - +
743A TYR* 3.5 10.0 - - - +
744A PRO* 3.7 12.9 - - - +
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Residues in contact with GLN 704 (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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662A SER* 4.8 0.2 + - - -
698A PRO* 2.5 30.6 + - + +
699A TRP* 4.2 6.7 + - - +
700A SER 2.9 15.0 + - - +
701A GLY* 3.5 11.9 - - - +
703A SER* 1.3 76.6 - - - +
705A ASN* 1.3 69.5 + - - +
706A PHE 3.2 0.7 + - - -
707A ALA* 3.2 7.3 + - - +
708A PRO* 3.2 19.8 - - - +
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Residues in contact with ASN 705 (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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662A SER* 3.1 27.9 + - - +
701A GLY* 2.8 30.3 + - - +
702A PRO* 4.1 9.1 - - + +
704A GLN* 1.3 77.3 - - - +
706A PHE* 1.3 60.4 + - + +
708A PRO* 3.7 2.1 - - - +
709A GLU* 4.7 5.2 + - - +
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Residues in contact with PHE 706 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
694A ASP* 3.9 15.9 - - - -
702A PRO 3.3 17.9 + - - +
703A SER 4.1 1.8 - - - +
704A GLN 3.1 1.0 - - - -
705A ASN* 1.3 76.0 - - + +
707A ALA* 1.3 55.7 + - - +
708A PRO 3.4 1.6 - - - -
709A GLU* 3.0 21.5 + - + -
710A PHE* 2.7 61.8 + + + -
713A LEU* 6.5 0.2 - - + -
744A PRO* 3.9 20.6 - - + -
746A VAL* 3.5 33.9 - - + -
766A ARG* 3.7 45.5 - - + -
768A ALA* 6.3 0.2 - - - -
771A ILE* 4.4 10.5 - - + -
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Residues in contact with ALA 707 (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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694A ASP* 4.8 3.8 - - - +
703A SER 3.1 13.4 + - - +
704A GLN* 3.6 10.5 - - - +
706A PHE* 1.3 76.2 - - - +
708A PRO* 1.4 70.7 - - + +
710A PHE* 3.2 8.9 + - - +
711A GLU* 3.1 28.9 + - + +
725A LYS* 4.1 21.5 + - - +
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Residues in contact with PRO 708 (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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662A SER* 3.5 24.9 - - - +
665A LEU* 3.7 17.0 - - + +
666A GLY* 3.5 33.0 - - - +
704A GLN 3.2 15.9 - - - +
705A ASN 3.7 5.6 - - - +
706A PHE 3.7 1.3 - - - -
707A ALA* 1.4 91.6 - - + +
709A GLU* 1.3 62.2 + - - +
711A GLU* 3.3 9.9 + - + +
712A LEU* 3.1 20.1 + - - +
715A ARG* 5.0 0.9 + - - -
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Residues in contact with GLU 709 (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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661A ARG* 2.9 44.6 + - - +
662A SER* 5.5 0.2 + - - -
665A LEU* 3.6 6.3 - - - +
705A ASN 4.7 3.5 + - - +
706A PHE* 3.0 23.9 + - + +
708A PRO* 1.3 80.3 - - - +
710A PHE* 1.3 57.1 + - - +
712A LEU* 3.0 21.9 + - - +
713A LEU* 3.1 10.6 + - - +
766A ARG 3.3 23.3 - - - +
767A ASP* 3.7 7.0 - - - +
768A ALA* 2.8 34.8 + - - +
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Residues in contact with PHE 710 (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 SER* 4.0 11.9 - - - -
692A VAL* 3.8 36.1 - - + -
693A VAL 4.4 2.0 - - - -
694A ASP* 3.5 37.7 - - + +
706A PHE* 2.7 40.8 + + + +
707A ALA* 3.2 8.9 + - - +
709A GLU* 1.3 72.1 - - - +
711A GLU* 1.3 65.5 + - - +
713A LEU* 3.2 18.5 + - + +
714A ALA* 2.9 24.4 + - - +
723A ALA* 4.1 5.2 - - + -
724A GLY 3.2 28.3 - - - -
725A LYS* 3.7 14.8 - - + -
746A VAL* 4.8 2.9 - - + -
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Residues in contact with GLU 711 (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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665A LEU 5.7 1.1 - - - +
668A LEU 5.2 2.9 - - - +
669A PRO 4.3 2.5 - - - +
670A GLN* 3.5 18.9 + - + +
671A ALA* 2.8 28.1 + - - -
672A SER* 2.6 34.9 + - - -
707A ALA 3.1 18.2 + - - +
708A PRO* 3.3 10.5 + - + +
710A PHE* 1.3 74.7 - - - +
712A LEU* 1.3 63.5 - - - +
714A ALA* 3.6 2.5 - - - +
715A ARG* 3.0 44.9 + - - +
725A LYS* 3.7 16.9 + - - +
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Residues in contact with LEU 712 (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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608A LEU* 3.8 38.6 - - + -
661A ARG* 3.4 29.2 - - - +
665A LEU* 4.1 11.4 - - + -
708A PRO 3.1 10.4 + - - +
709A GLU* 3.0 11.4 + - - +
711A GLU* 1.3 73.6 - - - +
713A LEU* 1.3 66.7 + - - +
715A ARG* 3.2 28.3 + - + +
716A MET* 2.9 41.9 + - + +
768A ALA* 3.7 16.8 - - + -
769A LYS* 6.1 2.2 - - + -
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Residues in contact with LEU 713 (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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692A VAL* 4.0 22.7 - - + -
706A PHE* 5.5 0.2 - - + -
709A GLU 3.1 11.1 + - - +
710A PHE* 3.2 27.1 + - + +
712A LEU* 1.3 77.3 - - - +
714A ALA* 1.3 61.6 - - - +
716A MET* 3.2 6.3 + - - +
717A ILE* 3.1 50.1 + - + +
746A VAL* 5.3 0.9 - - + -
768A ALA* 3.9 17.9 - - + +
771A ILE* 3.7 42.4 - - + -
772A ALA* 3.9 17.3 - - + +
775A ILE* 4.5 1.8 - - + -
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Residues in contact with ALA 714 (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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671A ALA* 3.7 18.4 - - + -
672A SER* 3.8 9.4 - - - +
710A PHE 2.9 12.9 + - - +
711A GLU* 3.6 11.2 - - - +
712A LEU 3.2 0.2 - - - -
713A LEU* 1.3 75.9 - - - +
715A ARG* 1.3 62.5 + - - +
717A ILE* 3.6 6.8 - - - +
718A LYS* 3.2 28.1 + - - +
721A VAL 5.0 0.5 - - - +
723A ALA* 3.6 32.1 - - + -
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Residues in contact with ARG 715 (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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665A LEU* 4.3 5.3 + - - +
668A LEU* 3.3 44.1 + - - +
669A PRO* 2.9 39.6 + - - +
671A ALA* 3.7 18.8 - - + -
708A PRO 5.2 0.4 + - - -
711A GLU* 3.0 39.3 + - - +
712A LEU* 3.6 31.4 - - + +
714A ALA* 1.3 74.5 - - - +
716A MET* 1.3 66.7 + - - +
717A ILE 3.3 0.3 + - - -
718A LYS* 3.4 17.6 + - - +
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Residues in contact with MET 716 (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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608A LEU* 5.5 4.7 - - + -
712A LEU* 2.9 40.7 + - + +
713A LEU* 3.6 5.8 - - - +
715A ARG* 1.3 74.8 - - + +
717A ILE* 1.3 65.5 + - + +
718A LYS 3.7 3.1 + - - +
768A ALA* 3.9 25.6 - - - +
769A LYS* 3.9 26.7 - - + -
772A ALA* 3.8 21.5 - - + -
776A TYR* 3.4 12.5 + - + +
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Residues in contact with ILE 717 (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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692A VAL* 3.9 27.1 - - + -
713A LEU* 3.1 40.2 - - + +
714A ALA* 3.6 9.0 - - - +
716A MET* 1.3 75.7 - - - +
718A LYS* 1.3 70.5 + - - +
720A LYS* 2.9 19.7 + - - +
721A VAL* 3.2 41.4 + - + +
722A ARG 5.0 0.4 - - - +
723A ALA* 5.0 1.1 - - + -
772A ALA* 4.1 13.0 - - + +
775A ILE* 4.9 5.6 - - + -
776A TYR* 3.6 30.3 - - + +
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Residues in contact with LYS 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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671A ALA* 3.8 34.7 + - + +
714A ALA* 3.2 18.0 + - + +
715A ARG* 3.6 13.9 - - - +
716A MET 3.4 4.7 - - - +
717A ILE* 1.3 77.9 - - - +
719A GLY* 1.3 62.3 + - - +
720A LYS* 4.8 2.4 - - - +
721A VAL 4.2 6.5 - - - +
722A ARG* 6.3 1.8 - - - +
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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