Contacts of the helix formed by residues 835 - 847 (chain A) in PDB entry 3E0D
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 835 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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635A VAL* 4.0 26.7 - - + -
639A LYS* 3.7 36.1 - - + -
641A VAL* 3.6 29.5 - - + +
643A LEU* 4.6 23.1 - - + -
830A TYR* 5.0 5.4 - + - -
831A VAL* 2.7 24.4 + - + +
832A LYS 4.3 3.6 - - - -
833A ALA 3.6 0.6 - - - -
834A HIS* 1.3 90.9 - - + +
836A PRO* 1.1 111.0 - - + +
838A GLU* 4.8 2.2 - - + -
839A PHE* 2.5 28.8 + - + +
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Residues in contact with PRO 836 (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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639A LYS* 4.6 9.9 - - - +
832A LYS 4.6 7.4 - - - +
833A ALA 5.2 2.0 - - - +
834A HIS 3.2 11.0 - - - +
835A TYR* 1.1 118.2 - - + +
837A VAL* 1.3 73.3 + - + +
838A GLU* 4.1 6.3 - - - +
839A PHE* 3.4 2.8 - - - +
840A MET* 3.2 19.4 + - - +
864A LEU* 5.7 10.6 - - + +
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Residues in contact with VAL 837 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
836A PRO* 1.3 81.4 - - + +
838A GLU* 1.3 71.4 + - - +
840A MET* 3.0 9.2 + - - +
841A ALA* 2.9 25.3 + - - +
866A ILE* 3.6 33.7 - - + -
882A VAL* 3.7 31.4 - - + -
885A GLU* 5.6 6.3 - - - +
886A GLU 5.7 0.4 - - - -
887A ILE* 3.7 22.3 - - + +
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Residues in contact with GLU 838 (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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631A ALA* 5.5 0.9 - - - -
634A ILE* 2.4 44.5 - - + +
635A VAL* 4.1 19.5 - - + +
638A SER* 2.1 40.8 + - - -
639A LYS* 4.1 16.2 + - - -
835A TYR* 4.8 4.7 - - + -
836A PRO* 4.1 2.8 - - - +
837A VAL* 1.3 89.1 + - - +
839A PHE* 1.3 56.0 + - - +
841A ALA* 3.1 7.7 + - - +
842A ALA* 2.7 38.4 + - - +
882A VAL* 4.9 10.3 - - + +
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Residues in contact with PHE 839 (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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627A PHE* 3.4 27.9 - + - -
631A ALA* 5.0 2.5 - - - -
635A VAL* 5.4 1.6 - - - +
828A THR* 2.6 36.6 - - + -
831A VAL* 1.7 59.9 - - + -
832A LYS* 2.4 44.2 - - + -
835A TYR* 2.5 32.2 + - + +
836A PRO 4.5 1.1 - - - -
838A GLU* 1.3 79.9 - - - +
840A MET* 1.3 64.5 + - + +
842A ALA* 3.1 4.2 + - - +
843A LEU* 2.9 39.6 + - + +
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Residues in contact with MET 840 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
832A LYS* 4.1 18.2 - - + +
836A PRO 3.2 9.5 + - - +
837A VAL* 3.0 11.2 + - - +
839A PHE* 1.3 90.0 - - + +
841A ALA* 1.3 58.2 + - - +
843A LEU* 3.2 31.3 + - + +
844A LEU* 2.9 34.6 + - + +
857A TYR* 4.0 13.0 - - + +
860A ASP* 4.4 8.3 - - + -
861A ALA* 3.5 44.2 - - + -
864A LEU* 4.8 11.0 - - + -
887A ILE* 5.0 6.1 - - + -
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Residues in contact with ALA 841 (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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634A ILE* 4.7 7.6 - - + +
837A VAL 2.9 13.0 + - - +
838A GLU* 3.6 11.9 - - - +
840A MET* 1.3 74.2 - - - +
842A ALA* 1.3 60.4 + - - +
844A LEU* 3.8 3.4 - - - -
845A SER* 2.9 27.4 + - - -
880A PHE* 3.3 37.2 - - + +
881A LYS* 4.8 0.7 - - - +
882A VAL* 4.5 14.4 - - + -
887A ILE* 4.8 7.5 - - + +
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Residues in contact with ALA 842 (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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627A PHE* 2.8 20.1 - - + -
630A GLU* 4.1 9.2 - - + -
631A ALA* 3.8 31.4 - - + +
634A ILE* 4.3 5.6 - - + +
838A GLU 2.7 18.8 + - - +
839A PHE 3.5 4.9 - - - +
841A ALA* 1.3 70.9 - - - +
843A LEU* 1.3 61.3 + - - +
844A LEU 3.2 0.2 - - - -
845A SER* 4.1 6.1 - - - -
846A VAL* 2.8 28.9 + - - +
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Residues in contact with LEU 843 (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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627A PHE* 2.4 48.2 - - + -
666A GLY* 3.2 46.4 - - - +
832A LYS* 5.1 0.4 - - - -
839A PHE* 2.9 18.8 + - + +
840A MET* 3.2 35.6 + - + +
842A ALA* 1.3 76.3 - - - +
844A LEU* 1.3 62.2 + - - +
846A VAL* 3.7 0.9 + - + +
847A GLU* 3.4 16.6 + - + +
857A TYR* 3.5 40.5 - - + +
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Residues in contact with LEU 844 (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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840A MET* 2.9 31.4 + - + +
841A ALA* 3.7 2.0 - - - +
843A LEU* 1.3 74.9 - - - +
845A SER* 1.3 63.4 + - - +
847A GLU 3.2 5.0 + - - -
848A ARG* 3.0 23.0 + - - -
854A VAL* 3.7 22.1 - - - +
857A TYR* 3.6 29.6 - - + +
858A ILE* 3.9 9.2 - - + -
861A ALA* 5.4 2.5 - - + -
868A VAL* 5.8 1.3 - - + -
880A PHE* 2.0 96.8 - - + -
887A ILE* 4.6 8.1 - - + -
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Residues in contact with SER 845 (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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471A ARG* 5.0 0.2 + - - -
630A GLU* 4.1 18.4 + - - +
633A ARG* 6.4 0.2 - - - -
634A ILE* 5.9 2.7 - - - -
841A ALA 2.9 19.4 + - - -
842A ALA* 3.6 8.5 - - - -
844A LEU* 1.3 74.9 - - - +
846A VAL* 1.3 64.8 + - - +
848A ARG* 3.1 25.0 + - - +
879A ASP* 1.6 63.8 + - - +
880A PHE 4.4 1.3 - - - -
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Residues in contact with VAL 846 (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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623A ARG* 2.8 68.9 + - + +
626A THR* 4.0 9.9 - - + +
627A PHE* 2.9 59.7 - - + +
630A GLU* 4.9 9.9 - - + -
842A ALA 2.8 15.2 + - - +
843A LEU* 4.2 2.5 - - + +
845A SER* 1.3 71.8 - - - +
847A GLU* 1.3 66.2 + - + +
848A ARG* 3.5 2.9 + - - +
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Residues in contact with GLU 847 (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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623A ARG* 4.9 11.2 - - - +
671A GLU* 5.5 0.5 - - - +
843A LEU* 3.4 9.9 + - + +
844A LEU 3.2 6.6 + - - -
846A VAL* 1.3 91.5 - - + +
848A ARG* 1.3 62.8 + - - +
849A HIS 3.2 3.1 - - - -
850A ASP* 3.2 22.7 + - + +
853A LYS* 3.4 32.3 + - + +
854A VAL* 3.4 11.1 + - - +
857A TYR* 3.6 36.3 + - + +
7C G 4.6 13.0 - - - +
8C T 4.8 2.9 + - - -
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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