Contacts of the helix formed by residues 900 - 910 (chain A) in PDB entry 4QMH
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 ASP 900 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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861A ILE* 4.6 5.1 + - - +
863A GLU* 4.8 8.3 - - - +
866A LEU* 4.0 22.7 - - + +
898A ILE 3.2 0.4 + - - -
899A GLY* 1.3 75.8 - - - +
901A LEU* 1.3 63.4 + - - +
902A ALA 3.3 2.7 - - - -
903A PRO* 3.3 20.1 - - + +
904A ALA* 3.5 13.0 + - - +
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Residues in contact with LEU 901 (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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857A ILE* 5.0 1.8 - - + -
861A ILE* 3.9 21.8 - - + +
865A LEU* 5.6 0.4 - - + -
866A LEU* 4.4 5.8 - - + -
869A MET* 4.0 18.6 - - + -
884A LEU* 3.9 36.6 - - + -
898A ILE* 3.0 37.5 + - + +
899A GLY 3.3 1.0 - - - -
900A ASP* 1.3 78.3 - - - +
902A ALA* 1.3 57.4 + - - +
904A ALA* 3.2 4.9 + - - +
905A LEU* 2.8 55.4 + - + +
927A LEU* 4.5 12.8 - - + -
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Residues in contact with ALA 902 (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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898A ILE* 4.1 9.0 - - + +
899A GLY 5.0 0.8 + - - +
901A LEU* 1.3 77.3 - - - +
903A PRO* 1.3 71.0 - - + +
905A LEU* 3.2 4.4 + - - -
906A ALA* 2.9 22.2 + - - +
938A HIS* 3.5 35.2 - - + +
941A ASN* 3.7 22.2 - - + +
942A LEU* 3.6 13.6 - - + +
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Residues in contact with PRO 903 (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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899A GLY 5.3 0.9 - - - +
900A ASP* 3.3 23.6 - - + +
902A ALA* 1.3 95.4 - - + +
904A ALA* 1.3 61.1 + - - +
906A ALA* 3.2 13.6 + - + +
907A HIS* 3.1 28.0 + - + +
941A ASN* 3.8 23.3 - - - +
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Residues in contact with ALA 904 (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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866A LEU* 3.7 27.4 - - + +
869A MET* 4.3 12.6 - - + -
900A ASP 3.5 11.2 + - - +
901A LEU* 3.2 9.5 + - - +
903A PRO* 1.3 81.5 - - - +
905A LEU* 1.3 62.7 + - - +
907A HIS* 3.4 15.0 + - - +
908A ARG* 3.4 20.3 + - - +
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Residues in contact with LEU 905 (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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869A MET* 4.0 12.3 - - + -
881A LEU* 4.4 4.7 - - + -
884A LEU* 3.8 23.8 - - + -
901A LEU* 2.8 45.6 + - + +
902A ALA* 3.2 5.8 + - - +
904A ALA* 1.3 70.2 - - - +
906A ALA* 1.3 65.5 + - - +
908A ARG* 3.0 4.9 + - + +
909A LEU* 2.9 25.3 + - - +
920A THR* 3.6 21.7 - - + +
923A ILE* 4.4 10.5 - - + -
924A CYS* 4.3 12.1 - - - -
927A LEU* 4.1 20.9 - - + -
942A LEU* 3.9 13.0 - - + -
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Residues in contact with ALA 906 (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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902A ALA 2.9 12.9 + - - +
903A PRO* 3.2 14.1 + - + +
905A LEU* 1.3 76.5 - - - +
907A HIS* 1.3 63.6 + - + +
909A LEU* 3.2 22.2 + - - +
910A VAL* 3.5 11.8 + - - +
941A ASN* 3.4 27.6 - - + +
942A LEU* 3.9 6.2 - - - +
945A GLY* 5.3 2.5 - - - +
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Residues in contact with HIS 907 (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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903A PRO* 3.1 26.9 + - + -
904A ALA* 3.6 10.2 + - - +
905A LEU 3.2 0.2 - - - -
906A ALA* 1.3 79.0 - - + +
908A ARG* 1.3 85.1 + - - +
910A VAL* 3.2 16.0 + - + +
911A ASP* 3.2 17.5 + - - -
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Residues in contact with ARG 908 (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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869A MET* 3.2 40.4 + - + -
870A SER* 3.8 18.0 - - - +
877A ARG* 3.7 17.6 - - - +
881A LEU* 4.7 6.3 - - + -
904A ALA 3.4 17.0 + - - +
905A LEU* 3.0 7.8 + - - +
907A HIS* 1.3 99.5 + - - +
909A LEU* 1.3 65.4 + - - +
910A VAL 3.1 1.8 - - - -
911A ASP* 2.7 50.3 + - - +
916A ILE* 4.0 9.9 - - + -
917A ALA* 3.4 12.1 - - - -
920A THR* 3.2 23.9 + - + +
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Residues in contact with LEU 909 (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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905A LEU 2.9 13.8 + - - +
906A ALA* 3.2 10.3 + - - +
908A ARG* 1.3 77.1 - - - +
910A VAL* 1.3 61.3 + - - +
911A ASP 3.4 0.4 - - - -
917A ALA* 3.7 16.1 - - - +
920A THR* 3.6 20.2 - - + -
921A LEU* 3.6 39.1 - - + +
924A CYS* 4.2 2.5 - - - -
942A LEU* 3.6 45.8 - - + +
945A GLY* 4.1 19.6 - - - +
946A PHE* 3.6 17.9 - - + -
948A HIS* 6.0 0.3 - - - -
949A ALA* 5.2 7.2 - - + +
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Residues in contact with VAL 910 (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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906A ALA 3.7 11.4 - - - +
907A HIS* 3.3 20.4 - - + +
909A LEU* 1.3 81.4 - - - +
911A ASP* 1.3 65.3 + - - +
912A SER* 3.7 1.2 + - - -
945A GLY* 4.4 17.5 - - - +
948A HIS* 4.3 26.2 - - + -
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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