Contacts of the helix formed by residues 869 - 879 (chain A) in PDB entry 4QUM
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 TYR 869 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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627A ALA* 2.3 35.2 + - + -
628A ASP* 3.5 13.7 - - + +
633A SER* 3.7 18.7 - - - -
636A GLN* 5.4 13.9 - - + -
861A LEU* 5.3 0.6 - - - +
867A PRO* 3.7 31.8 + - + +
868A ILE* 1.3 79.1 - - - +
870A PRO* 1.3 68.5 - - + +
871A LEU 3.2 2.9 - - - -
872A ASP* 2.9 38.9 + - + +
873A ILE* 3.2 16.2 + - - +
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Residues in contact with PRO 870 (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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637A LEU* 4.1 20.6 - - + -
854A THR* 4.8 6.0 - - + +
868A ILE* 3.7 11.4 - - + +
869A TYR* 1.3 84.0 - - + +
871A LEU* 1.3 57.0 + - - +
873A ILE* 3.2 14.0 + - + +
874A VAL* 2.9 33.3 + - - +
891A TYR* 3.6 17.5 - - + +
895A CYS* 4.0 23.6 - - - -
898A ILE* 4.1 22.7 - - + -
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Residues in contact with LEU 871 (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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646A VAL 5.2 0.2 - - - +
649A GLN* 4.0 33.7 - - + +
650A PHE* 3.7 33.4 - - + +
653A LEU* 3.8 26.9 - - + +
869A TYR* 3.1 1.4 + - + -
870A PRO* 1.3 77.0 - - - +
872A ASP* 1.3 63.9 + - - +
874A VAL* 3.9 2.3 - - + +
875A ARG* 3.0 44.1 + - - +
891A TYR* 3.3 18.1 + - + +
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Residues in contact with ASP 872 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
869A TYR* 2.9 33.6 + - + +
871A LEU* 1.3 78.3 - - - +
873A ILE* 1.3 59.9 + - + +
875A ARG* 3.4 33.7 + - - +
876A LYS* 3.0 30.7 + - - +
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Residues in contact with ILE 873 (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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703A MET* 3.6 24.2 - - + +
854A THR* 3.9 35.4 - - + +
857A THR* 3.9 26.5 - - + -
858A ALA* 4.6 4.5 - - + +
861A LEU* 4.1 9.9 - - + -
868A ILE* 4.1 24.2 - - + -
869A TYR 3.2 15.1 + - - +
870A PRO* 3.2 11.2 + - + +
872A ASP* 1.3 77.8 - - + +
874A VAL* 1.3 62.7 + - - +
876A LYS* 3.4 2.3 + - - -
877A MET* 3.1 24.1 + - + +
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Residues in contact with VAL 874 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
650A PHE* 4.5 6.3 - - + -
653A LEU* 3.7 13.5 - - + -
854A THR* 4.1 10.1 - - + +
870A PRO 2.9 20.5 + - - +
871A LEU* 3.9 5.4 - - + +
873A ILE* 1.3 75.3 - - - +
875A ARG* 1.3 56.5 + - - +
877A MET* 3.2 21.8 + - + +
878A ARG* 2.9 57.0 + - - +
884A MET 3.9 8.7 - - - +
885A VAL* 4.1 5.8 - - + -
891A TYR* 3.8 25.1 - - + -
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Residues in contact with ARG 875 (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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653A LEU* 4.0 22.5 - - + +
654A TYR* 3.4 31.2 - - + +
871A LEU* 3.0 36.1 + - - +
872A ASP* 3.4 34.6 + - - +
874A VAL* 1.3 75.6 - - - +
876A LYS* 1.3 59.6 + - - +
878A ARG* 3.1 5.0 + - - +
879A ASP* 2.9 40.9 + - - +
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Residues in contact with LYS 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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702A ASN 3.5 13.2 - - - -
703A MET* 4.0 16.6 - - + -
704A GLU* 3.3 54.7 + - - +
872A ASP 3.0 19.0 + - - +
873A ILE* 3.8 5.2 - - - +
874A VAL 3.3 0.2 - - - -
875A ARG* 1.3 77.1 - - - +
877A MET* 1.3 57.6 + - - +
879A ASP* 3.5 15.9 + - + +
880A GLN* 2.8 32.4 + - - +
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Residues in contact with MET 877 (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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701A VAL* 4.5 4.9 - - + +
703A MET* 3.6 19.1 - - + -
850A GLY* 3.6 10.1 - - - +
853A VAL* 3.5 33.0 - - + -
854A THR* 3.1 24.7 - - - +
873A ILE* 3.1 14.4 + - + +
874A VAL* 3.2 24.0 + - - +
876A LYS* 1.3 73.0 - - - +
878A ARG* 1.3 60.0 + - - +
879A ASP 3.1 1.8 - - - -
880A GLN* 2.8 26.2 + - - +
881A ARG* 2.9 15.3 + - - +
884A MET* 3.8 31.5 - - + +
885A VAL* 3.8 13.2 - - + -
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Residues in contact with ARG 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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650A PHE* 3.5 21.0 + - - -
653A LEU* 3.7 22.1 + - - +
654A TYR* 2.9 42.1 + - + -
655A ARG* 3.8 27.7 - - - +
657A LYS* 4.3 1.5 + - - -
682A TYR* 2.6 35.2 + - - -
874A VAL* 2.9 30.9 + - - +
875A ARG* 3.7 5.8 - - - +
877A MET* 1.3 74.6 - - - +
879A ASP* 1.3 56.3 + - - +
880A GLN 3.1 0.4 - - - -
881A ARG 3.3 9.7 - - - +
883A MET 4.0 9.1 + - - +
884A MET* 3.0 37.0 + - + +
885A VAL 3.4 16.6 + - - -
886A GLN 5.1 2.0 + - - -
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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
----------------------------------------------------------
654A TYR* 2.5 34.7 + - - -
657A LYS* 3.4 26.2 - - + +
660A LEU* 3.5 21.8 - - - +
682A TYR* 3.8 2.2 - - - -
685A THR* 4.6 3.8 - - - +
875A ARG* 2.9 28.0 + - - +
876A LYS* 3.6 11.9 - - - +
877A MET 3.1 0.8 - - - -
878A ARG* 1.3 76.3 - - - +
880A GLN* 1.3 61.1 + - + +
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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