Contacts of the helix formed by residues 923 - 932 (chain r) in PDB entry 6FF7
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 ALA 923 (chain r).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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629r GLU* 5.3 7.2 - - + +
633r ALA* 4.6 8.7 - - + -
664r PHE* 5.6 2.7 - - - +
893r MET* 5.8 3.4 - - + -
919r TRP 3.9 1.7 + - - +
920r LEU* 3.0 22.9 + - + +
921r GLY 3.4 0.4 - - - +
922r TYR* 1.3 81.4 - - - +
924r TYR* 1.3 65.9 + - - +
925r LEU* 3.2 13.7 - - + +
926r TYR* 3.1 18.0 + - - +
927r ILE* 3.6 4.9 + - - +
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Residues in contact with TYR 924 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
620r LEU* 6.0 5.8 - - + -
629r GLU* 4.9 18.1 - - + +
664r PHE* 4.7 22.1 - - + +
891r SER* 4.5 13.9 - - - -
922r TYR 4.1 0.4 + - - -
923r ALA* 1.3 72.8 - - - +
925r LEU* 1.3 63.1 + - - +
926r TYR 3.0 0.7 + - - -
927r ILE* 3.1 6.4 + - - +
928r ARG* 3.0 23.0 + - - +
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Residues in contact with LEU 925 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
629r GLU* 6.0 0.2 - - - +
891r SER* 4.0 15.3 - - - +
893r MET* 3.9 27.5 - - + +
894r VAL 5.6 0.9 - - - +
923r ALA* 4.0 7.8 - - + +
924r TYR* 1.3 78.1 - - - +
926r TYR* 1.3 56.8 + - - +
928r ARG* 3.9 5.7 - - - +
929r MET* 2.9 30.1 + - - +
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Residues in contact with TYR 926 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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920r LEU 3.4 22.0 - - - +
921r GLY* 4.1 16.4 - - - +
923r ALA* 3.1 14.4 + - - +
924r TYR 3.0 1.2 - - - -
925r LEU* 1.3 76.4 - - - +
927r ILE* 1.3 61.9 + - - +
929r MET* 3.3 6.2 + - - +
930r LEU* 2.9 27.6 + - - +
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Residues in contact with ILE 927 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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660r ASP* 4.8 14.3 - - + +
663r THR* 4.6 20.9 - - - -
664r PHE* 5.5 3.8 - - + +
923r ALA 3.6 4.9 + - - +
924r TYR* 3.1 8.6 + - - +
926r TYR* 1.3 79.9 - - - +
928r ARG* 1.3 57.8 + - - +
930r LEU* 3.3 7.3 + - - +
931r ARG* 2.9 30.8 + - - +
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Residues in contact with ARG 928 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
660r ASP* 6.0 3.1 - - - +
890r GLU* 5.6 5.2 - - + -
891r SER* 5.3 10.3 - - - +
924r TYR 3.0 16.3 + - - +
925r LEU* 4.1 7.2 - - - +
927r ILE* 1.3 76.0 - - - +
929r MET* 1.3 59.3 + - - +
931r ARG* 4.5 1.8 - - - +
932r SER* 2.8 37.1 + - - +
936r TYR* 5.1 3.1 - - + +
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Residues in contact with MET 929 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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925r LEU 2.9 21.6 + - - +
926r TYR* 3.6 6.1 - - - +
928r ARG* 1.3 75.9 - - - +
930r LEU* 1.3 61.4 + - - +
932r SER 4.4 0.2 - - - -
933r PRO* 3.6 21.1 - - - +
936r TYR* 4.4 21.3 - - + +
938r ILE* 5.5 1.2 - - - +
949r LEU* 6.1 5.2 - - + -
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Residues in contact with LEU 930 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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926r TYR 2.9 17.2 + - - +
927r ILE* 3.5 9.6 - - - +
928r ARG 3.1 0.2 - - - -
929r MET* 1.3 80.8 - - - +
931r ARG* 1.3 60.4 + - + +
932r SER 3.7 0.3 + - - -
933r PRO* 4.4 5.0 - - - +
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Residues in contact with ARG 931 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
927r ILE 2.9 15.6 + - - +
928r ARG* 4.8 0.9 - - - +
930r LEU* 1.3 77.7 - - + +
932r SER* 1.3 59.6 + - - +
933r PRO 4.0 0.4 - - - -
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Residues in contact with SER 932 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
928r ARG* 2.8 20.0 + - - +
931r ARG* 1.3 81.0 - - - +
933r PRO* 1.3 63.4 - - - +
934r THR* 3.2 5.2 - - - -
935r LEU* 3.1 23.0 + - - +
936r TYR* 3.5 8.7 + - - +
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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
------------------------------------------------------------
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