Contacts of the helix formed by residues 975 - 979 (chain A) in PDB entry 6DBT
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 ILE 975 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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812A THR* 5.3 4.0 + - - +
813A LEU* 3.7 33.3 - - + +
815A ALA* 3.6 19.5 - - + +
914A VAL 4.7 2.2 - - - +
915A TRP* 3.2 34.5 - - + +
917A SER 4.5 2.8 + - - -
920A PRO* 5.6 1.0 - - + +
965A VAL* 3.5 34.5 - - + +
968A ILE* 4.9 10.5 - - + -
969A VAL* 3.7 18.4 - - + -
972A ASP* 4.8 0.4 - - - -
974A SER* 1.3 89.3 + - - +
976A GLY* 1.3 66.2 + - - +
977A ALA 3.1 2.4 + - - -
978A TRP* 3.5 16.2 + - - +
979A ALA 4.4 1.2 + - - -
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Residues in contact with GLY 976 (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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669A ASN* 3.1 19.1 + - - -
815A ALA* 3.8 15.3 - - - -
915A TRP 3.9 2.5 + - - -
916A ARG 5.1 3.6 - - - -
917A SER 3.3 18.2 + - - -
918A THR* 5.7 1.1 - - - -
974A SER* 3.2 1.6 + - - -
975A ILE* 1.3 78.6 - - - +
977A ALA* 1.3 55.3 + - - +
978A TRP 2.8 8.2 + - - -
979A ALA* 2.9 14.3 + - - +
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Residues in contact with ALA 977 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
616A LYS* 4.7 2.1 - - - +
647A MET* 4.3 16.3 - - + +
664A GLN* 5.9 4.7 - - - +
668A PRO* 4.4 23.3 - - + +
669A ASN* 5.2 0.9 - - - -
917A SER 4.6 0.4 + - - -
918A THR* 4.6 10.6 + - + +
974A SER* 3.0 26.5 + - - +
975A ILE 3.1 0.6 - - - -
976A GLY* 1.3 73.6 - - - +
978A TRP* 1.3 85.4 + - + +
979A ALA 3.7 0.2 - - - -
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Residues in contact with TRP 978 (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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614A VAL* 3.9 19.5 - - + -
616A LYS* 3.6 33.1 - - + +
647A MET* 3.4 45.8 - - + -
725A ARG* 4.2 22.2 - - + +
727A THR* 2.9 47.0 + - + +
810A GLN* 5.6 1.5 + - - -
812A THR* 5.0 13.9 - - + +
813A LEU 5.7 2.4 - - - +
814A ASP* 5.3 0.2 - - - +
972A ASP* 2.7 44.4 + - - -
974A SER 4.8 0.4 - - - -
975A ILE 3.5 12.3 + - - +
976A GLY 3.0 1.2 - - - -
977A ALA* 1.3 97.2 - - + +
979A ALA* 1.3 67.3 + - - +
980A SER* 3.2 2.9 + - - -
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Residues in contact with ALA 979 (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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616A LYS* 4.5 13.3 + - - +
668A PRO 5.3 0.5 - - - +
669A ASN* 3.4 25.6 + - - +
814A ASP* 4.5 5.6 - - - +
815A ALA* 4.6 17.3 - - + +
816A LEU* 4.7 8.3 - - + +
975A ILE 4.4 0.4 + - - -
976A GLY* 2.9 10.5 + - - +
977A ALA 3.7 0.4 - - - -
978A TRP* 1.3 77.3 - - - +
980A SER* 1.3 64.2 + - - +
981A GLU* 3.2 15.4 + - + +
982A GLY* 3.8 6.8 + - - -
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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