Contacts of the helix formed by residues 831 - 841 (chain A) in PDB entry 2YD0
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 GLU 831 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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328A ARG* 3.3 22.4 + - - +
789A TYR* 4.3 5.4 - - - +
799A SER* 5.0 2.8 + - - -
802A GLU* 2.8 40.6 - - - +
827A ILE* 4.2 2.0 - - + -
828A LYS* 3.0 16.8 + - + +
829A THR 2.9 1.2 - - - -
830A GLN* 1.3 94.1 + - + +
832A PHE* 1.3 66.1 + - - +
833A PRO 3.3 2.7 - - - -
834A GLN* 3.1 20.8 + - - +
835A ILE* 2.9 34.3 + - + +
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Residues in contact with PHE 832 (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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818A LEU* 3.6 21.5 - - + -
821A SER* 3.3 32.3 - - - +
822A PHE* 3.6 14.4 - - + -
828A LYS 3.9 1.6 + - - -
829A THR* 2.8 24.2 + - + +
831A GLU* 1.3 75.8 - - - +
833A PRO* 1.3 65.9 - - + +
834A GLN 3.1 0.2 + - - -
835A ILE* 3.2 1.5 + - - +
836A LEU* 2.7 58.6 + - + +
852A PHE* 3.4 40.8 - + - -
860A LEU* 3.4 31.4 - - + -
864A PHE* 4.7 1.1 - + + -
874A MET* 3.9 7.2 - - - -
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Residues in contact with PRO 833 (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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829A THR 3.4 9.4 - - - +
830A GLN 3.7 9.0 - - - +
831A GLU 3.5 2.7 - - - -
832A PHE* 1.3 94.0 - - + +
834A GLN* 1.3 59.2 + - + +
836A LEU* 3.6 2.6 + - - +
837A THR* 3.2 23.0 + - - -
864A PHE* 3.7 25.8 - - + -
870A SER* 4.2 14.6 - - - +
873A HIS* 5.6 6.1 - - + +
874A MET* 4.0 34.0 + - + +
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Residues in contact with GLN 834 (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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799A SER* 4.2 12.5 + - - +
802A GLU* 4.0 8.8 - - + +
830A GLN 6.0 0.2 - - - +
831A GLU* 3.1 27.7 + - - +
833A PRO* 1.3 77.2 - - - +
835A ILE* 1.3 67.2 + - + +
837A THR* 3.1 8.6 + - - +
838A LEU* 2.8 56.4 + - + +
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Residues in contact with ILE 835 (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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802A GLU* 4.3 20.2 - - + +
806A CYS* 4.0 25.8 - - - -
817A LEU* 4.4 11.0 - - + +
818A LEU* 4.3 7.0 - - + -
821A SER* 3.9 22.4 - - - +
827A ILE* 3.8 37.7 - - + -
831A GLU* 2.9 24.2 + - + +
832A PHE* 3.7 4.9 - - - +
834A GLN* 1.3 79.6 - - + +
836A LEU* 1.3 62.3 + - - +
838A LEU* 3.3 3.3 + - + +
839A ILE* 3.0 37.4 + - + +
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Residues in contact with LEU 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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818A LEU* 3.7 24.7 - - + +
832A PHE* 2.7 43.8 + - + +
833A PRO 3.7 3.6 - - - +
835A ILE* 1.3 72.9 - - - +
837A THR* 1.3 58.2 + - - +
839A ILE* 3.5 0.3 + - - +
840A GLY* 3.1 22.2 + - - -
849A ALA* 3.5 36.1 - - + +
852A PHE* 4.6 6.1 - - + -
853A LEU* 4.4 13.2 - - + +
874A MET* 3.5 37.5 - - + -
878A THR* 3.8 16.0 - - + +
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Residues in contact with THR 837 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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833A PRO 3.2 11.0 + - - -
834A GLN* 3.1 12.7 + - + +
836A LEU* 1.3 78.2 - - - +
838A LEU* 1.3 71.2 + - + +
840A GLY* 3.2 2.3 + - - -
841A ARG* 3.0 30.5 + - + +
873A HIS* 3.5 24.3 + - - +
874A MET* 4.7 1.9 - - - -
877A GLY* 3.5 22.6 - - - +
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Residues in contact with LEU 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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802A GLU* 4.7 2.2 - - + +
803A PHE* 3.9 52.5 - - + +
806A CYS* 3.9 23.9 - - + +
807A ARG* 5.7 1.0 + - - -
834A GLN* 2.8 50.0 + - + +
835A ILE* 3.3 5.6 + - + +
837A THR* 1.3 75.4 - - + +
839A ILE* 1.3 57.4 + - - +
841A ARG* 3.1 32.1 + - + +
842A ASN* 3.1 11.8 + - - +
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Residues in contact with ILE 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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806A CYS* 4.0 15.5 - - + -
814A LEU* 3.4 50.7 - - + +
817A LEU* 4.3 6.3 - - + -
818A LEU* 3.6 25.6 - - + -
835A ILE* 3.0 23.6 + - + +
836A LEU 4.0 3.6 - - - +
838A LEU* 1.3 71.4 - - - +
840A GLY* 1.3 57.0 + - - +
841A ARG 3.1 4.3 - - - -
842A ASN* 3.0 20.2 + - - +
845A GLY* 3.1 37.3 - - - +
848A LEU* 4.8 1.3 - - + -
849A ALA* 4.1 9.0 - - + +
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Residues in contact with GLY 840 (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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689A LYS* 3.8 12.3 + - - -
836A LEU 3.1 13.5 + - - -
837A THR 3.2 5.3 + - - -
839A ILE* 1.3 74.5 - - - +
841A ARG* 1.3 57.0 + - - +
842A ASN 3.4 0.2 - - - -
846A TYR* 3.3 25.1 - - - +
849A ALA* 3.6 17.3 - - - +
877A GLY 4.0 16.0 - - - +
878A THR* 5.0 4.6 - - - -
881A GLN* 4.3 1.8 - - - +
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Residues in contact with ARG 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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681A ILE* 3.5 30.9 - - - +
684A TYR* 5.4 0.4 + - - -
685A LYS* 2.7 45.6 + - - +
688A GLU* 4.1 0.3 - - - +
689A LYS* 4.7 2.8 + - - +
807A ARG* 4.3 16.7 + - - +
837A THR* 3.0 20.2 + - + +
838A LEU* 3.2 26.7 - - + +
839A ILE 3.1 0.2 - - - -
840A GLY* 1.3 77.5 - - - +
842A ASN* 1.3 62.1 + - - +
843A PRO* 3.4 2.3 - - - +
877A GLY 6.1 0.2 - - - +
881A GLN* 3.3 34.2 - - - +
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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