Contacts of the helix formed by residues 930 - 937 (chain A) in PDB entry 6DMY
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 930 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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284A LYS* 6.2 0.3 - - - +
847A TYR 5.0 0.2 - - - +
851A TRP* 3.3 33.8 - - + +
926A TRP* 2.9 34.3 + - + +
927A VAL 4.8 0.9 - - - -
929A ASN* 1.3 79.5 - - - +
931A PRO* 1.3 62.2 - - - +
932A VAL* 3.9 10.6 - - - +
933A ALA* 3.3 29.4 + - - +
934A TYR* 3.3 17.8 + - - +
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Residues in contact with PRO 931 (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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207A GLY* 4.5 5.5 - - - +
208A GLU 4.7 5.6 - - - +
209A LEU* 3.7 37.9 - - + -
281A MET* 5.9 4.5 - - - -
927A VAL 4.8 5.6 - - - +
928A SER 4.3 13.0 - - - +
929A ASN 3.5 7.2 - - - +
930A ASP* 1.3 90.1 - - - +
932A VAL* 1.3 62.5 + - + +
934A TYR* 4.2 5.5 - - + +
935A ALA* 2.9 28.8 + - - +
1808A Y01 4.8 0.2 - - - +
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Residues in contact with VAL 932 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209A LEU* 4.1 18.6 - - + -
281A MET* 4.3 22.9 - - + -
284A LYS* 6.1 4.3 - - + -
285A ALA* 4.4 17.5 - - + +
334A TYR* 4.0 8.1 - - + +
930A ASP* 3.9 11.2 - - - +
931A PRO* 1.3 79.9 - - + +
933A ALA* 1.3 63.3 + - + +
935A ALA* 3.8 1.1 - - - +
936A ALA* 2.9 29.3 + - - +
1808A Y01 3.8 50.2 - - + +
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Residues in contact with ALA 933 (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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334A TYR* 4.2 17.5 - - - +
847A TYR* 3.9 18.6 - - + +
926A TRP* 4.0 12.2 - - - +
930A ASP* 3.3 28.3 + - - +
931A PRO 3.5 0.2 - - - -
932A VAL* 1.3 80.3 - - + +
934A TYR* 1.3 60.1 + - - +
936A ALA* 3.8 5.6 - - - -
937A SER* 3.1 29.3 + - - -
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Residues in contact with TYR 934 (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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207A GLY* 6.2 3.4 - - - -
926A TRP* 3.6 28.3 - + + -
927A VAL* 3.6 40.2 - - + +
930A ASP 3.3 17.3 + - - +
931A PRO* 4.2 4.5 - - + +
933A ALA* 1.3 77.6 - - - +
935A ALA* 1.3 61.9 + - - +
937A SER 2.9 21.6 - - - +
938A GLN* 5.0 0.3 - - - -
939A ALA* 3.1 21.0 + - + -
940A ASN* 3.8 3.9 - - - -
941A ILE* 3.0 48.3 + - + +
942A ARG* 4.5 3.1 + - - -
944A HIS* 5.8 0.3 + - - -
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Residues in contact with ALA 935 (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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206A SER* 4.4 5.7 - - - -
207A GLY* 4.0 28.0 - - - +
931A PRO 2.9 22.1 + - - +
932A VAL 4.0 0.7 - - - +
933A ALA 3.4 0.2 - - - -
934A TYR* 1.3 82.3 - - - +
936A ALA* 1.3 61.6 + - - +
937A SER 4.2 2.8 - - - -
938A GLN* 4.5 4.0 + - - +
1808A Y01 3.3 44.8 - - + +
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Residues in contact with ALA 936 (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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334A TYR* 3.5 43.3 - - + +
847A TYR* 4.7 4.7 - - + -
932A VAL 2.9 21.7 + - - +
933A ALA* 4.1 3.8 - - - +
934A TYR 3.3 0.2 - - - -
935A ALA* 1.3 75.6 - - - +
937A SER* 1.3 61.2 + - - +
938A GLN* 3.1 9.9 + - - +
1808A Y01 3.4 25.2 - - + +
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Residues in contact with SER 937 (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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842A LYS 4.5 4.2 + - - -
843A MET 4.3 0.9 - - - -
844A TRP* 3.4 34.1 + - - +
847A TYR* 3.5 25.0 - - - -
926A TRP* 5.0 2.0 - - - -
933A ALA 3.1 15.7 + - - -
934A TYR* 2.9 20.2 - - - +
935A ALA 4.2 0.2 - - - -
936A ALA* 1.3 76.3 - - - +
938A GLN* 1.3 52.0 + - - +
939A ALA* 2.6 22.8 + - - +
974A PHE* 5.8 0.7 - - - +
975A PRO* 5.4 5.4 - - - +
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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