Contacts of the helix formed by residues 868 - 883 (chain A) in PDB entry 1Q2L
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 868 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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542A PHE* 3.2 16.9 - - - -
866A PRO* 3.9 0.9 - - - +
867A GLN* 1.3 89.1 - - + +
869A LEU* 1.3 64.7 + - - +
870A GLY* 3.5 5.0 + - - -
871A GLU* 3.0 25.8 + - - +
872A GLU* 3.1 16.5 + - - +
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Residues in contact with LEU 869 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
539A SER* 4.0 17.0 - - - +
542A PHE* 3.6 19.2 - - + -
547A LYS* 3.5 22.2 - - + +
548A ALA* 3.5 43.1 - - - +
549A ASP* 4.1 6.1 - - + -
607A ASN* 3.8 14.1 - - - +
705A ILE* 3.9 20.2 - - + +
868A THR* 1.3 73.8 - - - +
870A GLY* 1.3 65.4 + - - +
872A GLU* 2.9 22.3 + - - +
873A ALA* 2.9 20.4 + - - +
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Residues in contact with GLY 870 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
549A ASP* 3.6 17.7 - - - +
607A ASN* 3.7 10.2 + - - +
868A THR* 3.2 6.2 + - - -
869A LEU* 1.3 79.3 - - - +
871A GLU* 1.3 55.7 + - - +
873A ALA* 3.3 3.3 + - - +
874A SER* 2.8 28.1 + - - -
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Residues in contact with GLU 871 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
864A GLN* 5.7 0.7 - - - +
865A ALA 5.0 0.9 - - - +
866A PRO* 3.8 11.6 - - + +
867A GLN* 2.7 39.7 + - - +
868A THR* 3.0 21.9 + - - +
870A GLY* 1.3 73.7 - - - +
872A GLU* 1.3 61.1 + - - +
874A SER* 3.2 9.1 + - - -
875A LYS* 2.9 50.5 + - + +
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Residues in contact with GLU 872 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
538A PRO 4.4 0.5 - - - +
539A SER* 2.7 29.4 + - - -
540A ARG* 3.0 32.6 + - - +
541A TYR* 3.7 20.3 + - + -
542A PHE* 3.7 9.6 - - + -
705A ILE* 3.9 15.3 - - + +
866A PRO* 3.5 17.9 - - + +
868A THR 3.1 8.8 + - - +
869A LEU* 2.9 12.1 + - + +
871A GLU* 1.3 77.0 - - - +
873A ALA* 1.3 62.6 + - - +
875A LYS* 3.3 14.1 + - + +
876A LEU* 3.4 28.8 + - + +
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Residues in contact with ALA 873 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
549A ASP* 3.4 39.7 - - + +
551A SER* 5.4 0.7 - - - +
703A MET* 3.5 22.4 - - + +
705A ILE* 4.6 8.9 - - + +
869A LEU 2.9 8.5 + - - +
870A GLY 3.6 5.4 - - - +
872A GLU* 1.3 77.6 - - - +
874A SER* 1.3 63.6 + - - +
876A LEU* 3.0 15.8 + - - -
877A SER* 3.0 12.7 + - - -
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Residues in contact with SER 874 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
870A GLY 2.8 17.9 + - - -
871A GLU* 3.2 12.5 + - - -
873A ALA* 1.3 78.0 - - - +
875A LYS* 1.3 60.3 + - - +
877A SER* 3.0 25.9 + - - -
878A LYS* 4.5 1.4 + - - +
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Residues in contact with LYS 875 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
861A GLN 5.3 2.4 + - - -
862A MET 5.0 3.2 + - - -
864A GLN* 3.4 30.3 + - - +
865A ALA 4.6 0.2 - - - -
866A PRO* 3.8 36.8 - - + -
871A GLU* 2.9 32.0 + - + +
872A GLU* 3.6 7.0 - - + +
873A ALA 3.2 0.2 - - - -
874A SER* 1.3 76.4 - - - +
876A LEU* 1.3 64.0 + - + +
878A LYS* 4.9 9.3 + - - +
879A ASP* 5.5 1.6 + - - +
890A ARG* 3.7 48.3 + - - +
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Residues in contact with LEU 876 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
523A PRO* 3.8 18.2 - - + -
703A MET* 4.1 11.2 - - - -
705A ILE* 3.8 36.6 - - + -
872A GLU* 3.4 25.6 - - + +
873A ALA* 3.0 7.5 + - - +
875A LYS* 1.3 83.2 - - + +
877A SER* 1.3 62.5 + - - +
878A LYS 3.3 3.3 + - - -
879A ASP* 3.5 3.8 + - - -
880A PHE* 3.1 21.7 + - - +
887A PHE* 3.5 30.3 - - + +
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Residues in contact with SER 877 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
603A MET* 5.3 14.1 - - - -
703A MET* 4.2 7.6 - - - -
873A ALA 3.0 11.1 + - - -
874A SER* 3.0 24.5 + - - -
876A LEU* 1.3 76.0 - - - +
878A LYS* 1.3 61.9 + - - +
880A PHE* 3.7 9.0 - - - +
881A ASP* 2.7 33.3 + - - +
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Residues in contact with LYS 878 (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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769A GLU* 5.0 11.4 - - - +
770A TYR* 5.6 2.7 - - - -
874A SER 4.5 2.3 + - - +
875A LYS 4.9 7.5 + - - +
876A LEU 3.3 0.8 - - - -
877A SER* 1.3 81.1 + - - +
879A ASP* 1.3 65.9 + - - +
881A ASP* 3.3 4.2 + - - +
882A ARG* 2.9 47.4 + - - +
889A SER* 2.9 36.5 + - - -
890A ARG* 5.2 8.3 - - - +
893A ILE* 6.0 4.7 - - - +
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Residues in contact with ASP 879 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
770A TYR* 4.3 1.4 + - - -
875A LYS 5.5 1.4 + - - +
876A LEU* 3.5 3.8 + - - +
878A LYS* 1.3 83.2 + - - +
880A PHE* 1.3 58.5 + - - +
882A ARG* 3.7 7.0 + - - +
883A GLY 3.0 7.1 + - - -
884A ASN* 2.8 58.9 + - - +
887A PHE* 3.3 34.2 - - + +
889A SER* 2.7 46.8 + - - -
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Residues in contact with PHE 880 (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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533A ARG* 5.7 1.6 - - + -
535A VAL* 3.6 26.2 - - + -
551A SER* 4.7 8.7 - - - -
553A ILE* 3.7 27.1 - - + -
555A ARG* 4.6 1.8 + - - -
603A MET* 5.3 2.9 - - + -
701A GLU* 3.7 31.8 - - + +
702A PHE 3.4 35.9 - - - -
703A MET* 3.7 34.3 - - + -
876A LEU 3.1 17.3 + - - +
877A SER* 3.7 7.6 - - - +
878A LYS 3.2 0.2 - - - -
879A ASP* 1.3 77.6 - - - +
881A ASP* 1.3 63.9 + - - +
883A GLY* 3.1 13.0 + - - -
885A MET* 4.3 4.6 - - + +
887A PHE* 3.8 10.0 - - + -
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Residues in contact with ASP 881 (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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553A ILE* 3.6 5.0 - - + +
555A ARG* 2.6 49.2 + - - +
599A ASN* 3.0 31.1 + - - +
603A MET* 6.1 1.6 - - + -
701A GLU* 5.4 0.2 - - - +
734A ASN* 4.0 9.2 + - - -
877A SER 2.7 23.7 + - - +
878A LYS* 3.6 5.6 - - - +
880A PHE* 1.3 79.2 - - - +
882A ARG* 1.3 67.3 + - - +
883A GLY 3.5 0.5 + - - -
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Residues in contact with ARG 882 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
734A ASN* 5.8 0.4 - - - +
736A ASP* 5.2 0.8 + - - +
769A GLU* 2.8 34.9 + - - -
770A TYR* 4.5 13.3 + - - -
810A ARG* 2.7 44.9 - - - +
878A LYS* 2.9 37.9 + - - +
879A ASP* 3.5 11.4 + - - +
881A ASP* 1.3 85.3 - - - +
883A GLY* 1.3 61.5 + - - +
884A ASN* 3.4 7.9 + - - +
959A GLU* 3.5 31.0 + - - +
960A LYS 6.2 0.5 - - - -
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Residues in contact with GLY 883 (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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879A ASP 3.0 5.1 + - - -
880A PHE 3.1 11.7 + - - -
881A ASP 3.3 1.4 + - - -
882A ARG* 1.3 79.3 - - - +
884A ASN* 1.3 59.4 + - - +
885A MET* 3.2 22.4 + - - +
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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
------------------------------------------------------------
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