Contacts of the helix formed by residues 873 - 891 (chain A) in PDB entry 1YGR
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 VAL 873 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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632A PHE* 3.6 6.3 - - - -
797A HIS* 3.6 26.7 - - + +
871A VAL 3.2 2.5 + - - +
872A GLN* 1.3 104.3 - - + +
874A GLU* 1.3 71.3 + - - +
875A ALA* 3.1 28.3 - - + +
876A GLN* 2.8 22.4 + - + +
877A TYR* 2.8 32.6 + - - +
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Residues in contact with GLU 874 (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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629A LEU* 3.6 34.1 - - + -
632A PHE* 3.0 38.7 - - + -
633A GLN* 6.2 0.7 - - - +
872A GLN 3.9 3.3 - - - +
873A VAL* 1.3 90.5 - - - +
875A ALA* 1.3 56.2 + - - +
877A TYR* 3.2 4.2 - - - +
878A ILE* 2.8 42.1 + - + +
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Residues in contact with ALA 875 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
797A HIS 5.5 0.4 - - - +
798A GLY* 5.2 1.3 - - - +
799A VAL* 3.7 22.4 - - + +
873A VAL* 3.0 16.7 - - + +
874A GLU* 1.3 77.1 + - - +
876A GLN* 1.3 60.1 + - - +
878A ILE* 3.4 9.5 + - - +
879A LEU* 2.8 27.0 + - - +
882A GLN* 5.0 1.2 + - - -
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Residues in contact with GLN 876 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
794A TRP* 4.2 10.1 - - + +
797A HIS* 4.0 14.5 - - - +
798A GLY 2.9 29.0 + - - +
799A VAL* 4.1 2.5 - - + -
833A GLY* 3.9 3.6 - - - +
834A ARG* 4.2 15.4 - - - +
837A THR* 3.4 27.8 + - + +
871A VAL* 4.6 3.8 - - + -
872A GLN* 3.5 17.0 + - - +
873A VAL* 2.8 36.4 + - + +
875A ALA* 1.3 74.3 - - - +
877A TYR* 1.3 66.3 + - - +
879A LEU* 3.1 10.8 + - + +
880A ILE* 3.0 29.0 + - - +
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Residues in contact with TYR 877 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
628A PHE* 3.7 22.0 - + - -
631A GLU* 3.0 39.9 + - + +
632A PHE* 3.4 32.1 - + + -
635A ILE* 3.7 24.0 - - + -
856A VAL* 4.6 2.9 - - + +
857A TYR* 3.3 16.3 + - - -
860A VAL* 4.2 13.9 - - + -
871A VAL* 4.2 15.4 - - + +
873A VAL 2.8 11.9 + - - +
874A GLU* 3.2 15.7 - - - +
876A GLN* 1.3 79.0 - - - +
878A ILE* 1.3 66.1 + - + +
879A LEU 3.0 1.0 + - - -
880A ILE* 3.2 11.9 + - + +
881A HIS* 3.0 42.7 + + - -
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Residues in contact with ILE 878 (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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617A TYR* 4.3 17.3 - - + +
621A ILE* 4.4 6.7 - - + -
624A GLU* 5.4 7.4 - - - +
625A GLY* 5.2 6.3 - - - +
628A PHE* 4.2 35.4 - - + -
629A LEU* 5.7 3.6 - - + +
874A GLU* 2.8 30.3 + - + +
875A ALA* 3.8 6.7 - - - +
877A TYR* 1.3 76.9 - - + +
879A LEU* 1.3 62.0 + - - +
881A HIS* 3.4 11.3 + - - +
882A GLN* 3.2 38.6 + - - +
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Residues in contact with LEU 879 (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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794A TRP* 4.5 7.4 - - + -
799A VAL* 3.4 35.4 - - + -
800A PRO* 3.5 17.7 - - + -
803A PRO* 5.0 14.4 - - + -
806A LEU* 3.3 31.0 - - + -
837A THR* 4.6 3.1 - - + -
841A ILE* 4.3 6.5 - - + -
875A ALA 2.8 13.1 + - - +
876A GLN* 3.1 13.9 - - - +
877A TYR 3.0 0.4 - - - -
878A ILE* 1.3 74.6 - - - +
880A ILE* 1.3 67.1 + - - +
882A GLN* 2.9 17.7 + - - +
883A ALA* 2.8 24.4 + - + +
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Residues in contact with ILE 880 (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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837A THR* 4.1 24.7 - - + +
840A GLY* 4.3 13.0 - - - +
841A ILE* 4.3 19.7 - - + +
844A MSE 4.8 1.6 - - + -
856A VAL* 4.3 15.3 - - + -
860A VAL* 4.7 14.4 - - + -
871A VAL* 4.3 29.6 - - + -
876A GLN 3.0 15.8 + - - +
877A TYR* 3.5 8.3 - - - +
879A LEU* 1.3 74.8 - - - +
881A HIS* 1.3 64.3 + - + +
883A ALA* 3.3 9.6 - - - +
884A LEU* 3.2 33.9 + - + +
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Residues in contact with HIS 881 (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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608A ILE* 5.4 10.2 - - + +
613A LEU* 5.7 6.7 - - + +
617A TYR* 4.3 7.0 - - + -
620A LYS* 5.7 0.9 - - - -
628A PHE* 3.3 37.8 - + + -
631A GLU* 4.0 12.3 - - - -
856A VAL* 3.5 36.8 - - + +
877A TYR* 3.0 50.5 - + - -
878A ILE* 3.5 6.7 - - - +
879A LEU 3.1 0.4 - - - -
880A ILE* 1.3 74.9 - - - +
882A GLN* 1.3 54.3 + - - +
884A LEU* 2.9 11.5 + - - +
885A VAL* 2.7 41.5 + - + +
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Residues in contact with GLN 882 (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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617A TYR* 3.3 27.5 + - + +
803A PRO* 3.5 28.9 - - + +
875A ALA 5.0 1.2 + - - -
878A ILE* 3.2 37.1 + - - +
879A LEU* 2.9 14.0 + - - +
881A HIS* 1.3 78.7 - - - +
883A ALA* 1.3 57.1 + - - +
885A VAL* 3.6 9.8 - - - +
886A GLU* 2.8 40.0 + - + +
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Residues in contact with ALA 883 (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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803A PRO* 4.4 4.4 - - + +
807A LEU* 3.5 33.3 - - + +
841A ILE* 3.7 37.9 - - + -
879A LEU* 2.8 13.9 + - + +
880A ILE 3.3 12.1 - - - +
882A GLN* 1.3 77.1 - - - +
884A LEU* 1.3 57.2 + - - +
886A GLU 4.0 0.2 - - - -
887A TYR* 3.0 22.7 + - - +
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Residues in contact with LEU 884 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
613A LEU* 3.7 14.8 - - + +
841A ILE* 4.7 3.1 - - + +
844A MSE 3.7 33.2 - - + +
845A LEU* 3.4 32.3 - - + -
848A LEU* 4.5 11.4 - - + +
854A VAL* 4.5 11.7 - - + -
856A VAL* 3.7 30.1 - - + -
880A ILE* 3.2 19.5 - - + +
881A HIS* 2.9 9.0 + - - +
883A ALA* 1.3 75.7 - - + +
885A VAL* 1.3 59.3 + - - +
886A GLU 3.2 0.2 - - - -
887A TYR* 4.2 0.6 - - - +
888A ASN* 2.9 33.4 + - - +
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Residues in contact with VAL 885 (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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613A LEU* 4.0 22.7 - - + -
614A LEU* 3.6 36.5 - - + +
617A TYR* 3.7 40.4 - - + -
881A HIS* 2.7 30.6 + - + +
882A GLN* 3.2 7.4 + - - +
884A LEU* 1.3 72.6 - - - +
886A GLU* 1.3 59.6 + - + +
888A ASN* 3.6 1.6 - - - +
889A GLN* 3.0 28.6 + - - +
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Residues in contact with GLU 886 (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 ASP* 4.0 9.5 - - - +
803A PRO* 3.5 32.3 - - + +
804A HIS* 4.1 8.0 + - - +
807A LEU* 5.0 4.0 - - + -
882A GLN* 2.8 20.7 + - + +
883A ALA* 4.1 2.7 - - - +
885A VAL* 1.3 81.5 - - + +
887A TYR* 1.3 64.3 + - - +
888A ASN 3.1 1.6 - - - -
889A GLN* 4.2 3.6 - - - -
890A PHE* 3.0 43.9 + - + +
891A GLY 3.7 2.8 + - - +
1174A GLN* 5.6 2.5 + - - +
1177A LYS* 4.5 13.0 + - - -
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Residues in contact with TYR 887 (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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807A LEU* 3.9 25.0 - - + +
810A ARG* 5.6 4.0 - - - -
845A LEU* 4.3 18.8 - - + -
848A LEU* 5.2 7.6 - - + -
849A GLU* 3.8 31.4 + - + +
883A ALA 3.0 19.5 + - - +
884A LEU 4.2 1.8 - - - +
886A GLU* 1.3 72.9 - - - +
888A ASN* 1.3 65.9 + - - +
891A GLY* 2.7 42.4 + - - +
892A GLU* 3.9 43.4 + - + +
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Residues in contact with ASN 888 (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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610A ALA* 3.2 37.2 - - - +
611A ASP* 4.5 1.9 - - - +
613A LEU* 3.3 17.7 - - + +
614A LEU* 4.9 3.3 + - - +
848A LEU* 4.4 16.2 - - + +
884A LEU 2.9 20.4 + - - +
885A VAL* 3.6 4.9 - - - +
887A TYR* 1.3 87.0 - - - +
889A GLN* 1.3 68.4 + - - +
891A GLY* 3.7 3.1 + - - -
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Residues in contact with GLN 889 (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 LEU* 4.1 26.8 - - + +
885A VAL 3.0 16.9 + - - +
886A GLU* 3.9 6.5 - - - +
888A ASN* 1.3 83.9 - - - +
890A PHE* 1.3 91.5 + - + +
925A ARG* 3.9 22.2 - - - +
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Residues in contact with PHE 890 (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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886A GLU* 3.0 34.4 + - + +
888A ASN 4.3 0.2 - - - -
889A GLN* 1.3 101.9 - - + +
891A GLY* 1.3 68.1 + - - +
892A GLU 3.9 0.2 + - - -
893A THR* 4.3 13.6 - - - +
925A ARG* 3.6 36.6 + - + +
927A PRO* 3.4 34.5 - - + -
1173A PHE* 3.7 30.9 - + + -
1174A GLN* 4.9 8.5 - - - +
1177A LYS* 3.9 23.3 - - + -
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Residues in contact with GLY 891 (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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804A HIS* 6.1 1.2 - - - -
886A GLU 3.7 0.5 + - - +
887A TYR* 2.7 49.5 + - - +
888A ASN 3.7 2.0 + - - -
889A GLN 3.6 0.8 - - - -
890A PHE* 1.3 80.3 - - - +
892A GLU* 1.3 59.2 + - - -
893A THR* 3.7 5.7 + - - -
1174A GLN* 5.5 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
------------------------------------------------------------
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