Contacts of the helix formed by residues 875 - 889 (chain A) in PDB entry 3SQD
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 GLU 875 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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874A PHE* 1.3 75.1 - - - +
876A PRO* 1.3 80.6 - - + +
877A VAL* 3.2 11.9 - - + +
878A GLN* 3.1 33.8 + - + +
879A VAL* 3.1 10.6 + - - +
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Residues in contact with PRO 876 (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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874A PHE 3.6 4.2 - - - +
875A GLU* 1.3 94.7 - - + +
877A VAL* 1.3 65.2 + - + +
879A VAL* 3.3 9.3 + - + +
880A GLN* 3.0 36.5 + - - +
137C GLN* 3.4 42.2 - - + +
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Residues in contact with VAL 877 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
875A GLU* 4.4 10.5 - - + +
876A PRO* 1.3 75.7 - - + +
878A GLN* 1.3 75.5 + - + +
880A GLN* 3.3 21.7 + - - +
881A GLN* 3.2 35.8 + - - +
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Residues in contact with GLN 878 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
874A PHE* 3.8 19.2 - - + +
875A GLU* 3.1 39.5 + - + +
877A VAL* 1.3 85.2 - - + +
879A VAL* 1.3 57.6 - - - +
881A GLN* 3.1 16.1 + - - +
882A TYR* 2.9 60.3 + - + -
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Residues in contact with VAL 879 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
871A PHE* 4.3 24.9 - - + -
874A PHE* 3.6 31.6 - - + +
875A GLU 3.1 9.1 + - - +
876A PRO* 3.6 12.1 - - + +
877A VAL 3.2 0.2 - - - -
878A GLN* 1.3 81.0 - - - +
880A GLN* 1.3 58.7 + - + +
882A TYR* 3.3 7.0 + - - +
883A ILE* 2.8 50.7 + - + +
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Residues in contact with GLN 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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876A PRO* 3.0 37.0 + - - +
877A VAL* 3.4 20.2 - - - +
879A VAL* 1.3 77.3 - - + +
881A GLN* 1.3 58.9 + - + +
883A ILE* 3.3 9.4 + - - +
884A LYS* 3.0 47.5 + - - +
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Residues in contact with GLN 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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877A VAL* 3.5 23.1 + - - +
878A GLN* 3.1 17.3 + - - +
880A GLN* 1.3 79.6 - - + +
882A TYR* 1.3 68.4 + - + +
883A ILE 3.3 0.2 + - - -
884A LYS* 3.3 14.7 + - + +
885A LYS* 3.1 39.3 + - - +
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Residues in contact with TYR 882 (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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871A PHE* 3.7 31.6 - + + -
874A PHE* 3.9 26.7 - + - -
878A GLN* 2.9 43.7 + - + -
879A VAL* 3.6 9.0 - - - +
881A GLN* 1.3 78.3 - - + +
883A ILE* 1.3 57.9 + - - +
885A LYS* 3.3 9.1 + - + +
886A LEU* 2.8 28.4 + - - +
927A PRO* 3.4 32.3 - - + +
930A LEU* 3.6 20.3 - - + +
931A GLU* 3.6 31.1 + - + +
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Residues in contact with ILE 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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871A PHE* 3.9 13.5 - - + -
879A VAL* 2.8 38.2 + - + +
880A GLN* 3.6 7.6 - - - +
881A GLN 3.2 0.2 - - - -
882A TYR* 1.3 72.6 - - - +
884A LYS* 1.3 69.3 + - + +
886A LEU* 3.0 15.4 + - - +
887A TYR* 3.0 37.9 + - + -
893A VAL* 3.8 25.6 - - + -
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Residues in contact with LYS 884 (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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880A GLN* 3.0 36.3 + - - +
881A GLN* 3.6 16.0 - - + +
883A ILE* 1.3 77.8 - - + +
885A LYS* 1.3 63.6 + - + +
887A TYR* 3.4 4.4 + - - +
888A ILE* 3.1 34.4 + - + +
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Residues in contact with LYS 885 (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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881A GLN* 3.1 25.4 + - - +
882A TYR* 3.5 15.7 - - + +
884A LYS* 1.3 75.5 - - + +
886A LEU* 1.3 66.8 - - - +
888A ILE* 3.4 3.3 + - - +
889A LEU* 3.2 28.4 + - - +
930A LEU* 4.7 9.4 - - + +
931A GLU* 3.4 34.1 + - - +
934A PHE* 3.5 57.5 - - + -
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Residues in contact with LEU 886 (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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867A PRO* 4.9 0.4 - - + +
869A VAL* 3.8 31.2 - - + -
871A PHE* 4.4 7.4 - - + -
882A TYR 2.8 14.7 + - - +
883A ILE* 3.0 8.7 + - - +
885A LYS* 1.3 77.0 - - - +
887A TYR* 1.3 61.0 + - + +
889A LEU* 3.1 11.8 + - - +
891A GLY* 2.9 45.0 + - - -
892A GLU* 3.3 31.6 - - - +
893A VAL* 3.7 15.0 - - + +
929A TRP* 5.6 0.7 - - + -
930A LEU* 4.3 18.4 - - + +
939A PHE* 4.1 15.0 - - + -
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Residues in contact with TYR 887 (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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859A MET 4.6 3.1 - - - +
883A ILE* 3.0 45.8 + - + +
884A LYS* 4.0 4.9 - - - +
886A LEU* 1.3 75.3 - - + +
888A ILE* 1.3 61.8 + - + +
889A LEU 3.1 1.6 - - - -
890A GLY* 2.9 18.5 + - - -
891A GLY 3.4 16.6 - - - -
892A GLU* 3.7 20.0 + - + +
893A VAL* 3.1 41.4 + - + +
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Residues in contact with ILE 888 (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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859A MET* 3.1 34.7 - - - +
884A LYS* 3.1 25.0 + - + +
885A LYS* 3.7 5.6 - - - +
887A TYR* 1.3 76.1 - - - +
889A LEU* 1.3 58.5 + - + +
890A GLY 3.4 0.3 + - - -
934A PHE* 4.0 25.8 - - + -
937A GLN* 4.0 22.1 + - - +
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Residues in contact with LEU 889 (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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859A MET* 4.0 11.8 + - - +
861A LEU* 3.8 7.6 - - - +
885A LYS 3.2 15.6 + - - +
886A LEU 3.1 8.9 + - - +
887A TYR 3.1 0.8 - - - -
888A ILE* 1.3 76.5 - - - +
890A GLY* 1.3 56.9 + - - +
930A LEU* 3.9 11.7 - - + -
933A CYS* 3.6 34.8 - - + +
934A PHE* 3.8 17.0 - - + +
937A GLN* 3.6 45.3 - - - +
938A LYS* 3.7 5.3 - - - +
939A PHE* 3.3 34.4 - - + -
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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
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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