Contacts of the helix formed by residues 811 - 827 (chain A) in PDB entry 3UGM
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 GLY 811 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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809A ASN* 3.2 4.3 - - - +
810A ASN* 1.4 78.0 - - - +
812A GLY* 1.4 50.3 + - - +
813A LYS* 2.7 19.8 + - - +
814A GLN* 3.0 20.6 + - - +
815A ALA* 3.7 12.8 - - - -
843A ASN 5.2 1.6 - - - -
844A GLY 3.8 16.6 + - - -
846A GLY* 5.1 3.6 - - - -
847A LYS* 5.8 1.3 - - - -
15B T 4.7 0.9 + - - -
16B G 3.7 18.5 + - - -
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Residues in contact with GLY 812 (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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777A GLY 5.6 1.3 - - - -
781A ALA* 3.9 13.2 - - - -
806A ILE 4.5 2.6 + - - -
807A ALA* 3.4 26.6 + - - -
809A ASN* 2.9 12.6 + - - +
810A ASN 4.0 2.0 - - - -
811A GLY* 1.4 68.5 - - - +
813A LYS* 1.3 56.9 - - - -
815A ALA* 3.0 20.9 - - - +
816A LEU* 3.2 21.6 - - - +
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Residues in contact with LYS 813 (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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777A GLY 5.6 0.2 + - - -
780A GLN* 2.7 56.4 - - + +
781A ALA* 4.3 3.8 - - - +
783A GLU* 5.3 2.6 + - - +
784A THR* 3.2 33.8 + - + +
787A ARG* 4.1 18.7 - - - +
810A ASN 4.8 0.4 + - - -
811A GLY 2.7 4.6 + - - -
812A GLY* 1.3 66.7 - - - +
814A GLN* 1.3 63.5 + - - +
815A ALA 2.6 15.2 + - - -
816A LEU* 3.1 13.7 + - - +
817A GLU* 3.2 16.4 + - + +
15B T 3.9 18.0 + - - +
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Residues in contact with GLN 814 (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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811A GLY* 3.0 9.5 + - - +
813A LYS* 1.3 81.7 - - - +
815A ALA* 1.3 58.5 + - - +
817A GLU* 4.3 9.3 - - - +
818A THR* 2.7 30.9 + - - -
821A ARG* 5.8 0.2 - - - +
847A LYS* 3.2 44.8 + - + +
14B C 4.4 0.4 + - - -
15B T 2.3 50.8 + - - +
16B G 4.1 13.7 - - - +
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Residues in contact with ALA 815 (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 ILE* 3.7 28.5 - - + +
811A GLY* 3.4 14.2 + - - -
812A GLY 3.0 20.4 - - - +
813A LYS 2.6 5.3 + - - -
814A GLN* 1.3 75.8 - - - +
816A LEU* 1.3 60.6 + - - +
818A THR* 3.7 2.4 - - - -
819A VAL* 2.9 29.2 + - - +
841A ALA* 4.8 8.1 - - + +
846A GLY* 5.6 2.7 - - - -
847A LYS 4.9 9.4 - - - +
850A LEU* 4.4 2.6 - - - +
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Residues in contact with LEU 816 (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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781A ALA 4.8 0.9 - - - +
784A THR* 4.0 32.3 - - + +
785A VAL* 4.7 3.1 - - + +
788A LEU* 3.9 20.6 - - + -
789A LEU* 6.0 2.5 - - - +
798A LEU* 6.2 1.6 - - + -
803A VAL* 4.4 27.1 - - + -
806A ILE* 4.1 19.7 - - + -
807A ALA* 3.8 16.8 - - + -
812A GLY 3.2 22.2 - - - +
813A LYS 3.1 1.7 + - - +
815A ALA* 1.3 70.9 - - - +
817A GLU* 1.3 60.1 + - - +
819A VAL* 2.5 35.0 + - + +
820A GLN* 2.9 13.2 + - - +
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Residues in contact with GLU 817 (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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784A THR* 5.2 0.9 - - + -
787A ARG* 4.1 25.0 + - - +
788A LEU* 3.8 15.4 - - + +
813A LYS* 3.2 16.7 + - + +
814A GLN* 4.3 7.4 - - - +
816A LEU* 1.3 79.1 - - - +
818A THR* 1.3 59.7 + - - +
820A GLN* 3.4 27.1 + - - +
821A ARG* 3.2 36.9 + - - +
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Residues in contact with THR 818 (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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814A GLN 2.7 23.7 + - - -
815A ALA 3.7 2.5 - - - -
816A LEU 3.1 0.6 - - - -
817A GLU* 1.3 74.1 - - - +
819A VAL* 1.3 61.4 + - - +
821A ARG* 2.8 36.7 + - - +
822A LEU* 2.8 43.0 + - + +
847A LYS* 3.2 13.3 - - - +
850A LEU* 3.7 22.9 - - + -
851A GLU* 4.0 15.0 - - + -
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Residues in contact with VAL 819 (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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798A LEU* 5.0 14.4 - - + -
806A ILE* 4.0 23.3 - - + -
815A ALA 2.9 17.0 + - - +
816A LEU* 2.5 23.9 + - + +
818A THR* 1.3 69.6 - - - +
820A GLN* 1.3 61.1 + - - +
822A LEU* 5.2 0.7 - - - -
823A LEU* 2.6 56.0 + - + +
837A VAL* 4.5 11.9 - - + -
841A ALA* 4.1 15.5 - - + -
850A LEU* 4.3 8.5 - - + -
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Residues in contact with GLN 820 (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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788A LEU* 4.2 24.5 - - + +
816A LEU 2.9 10.9 + - - +
817A GLU* 3.4 36.3 + - - +
819A VAL* 1.3 79.5 - - - +
821A ARG* 1.3 86.3 + - - +
822A LEU 3.0 0.5 + - - -
823A LEU* 4.8 2.7 - - - -
824A PRO* 3.1 21.5 - - - +
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Residues in contact with ARG 821 (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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814A GLN* 5.8 0.4 - - - +
817A GLU* 3.2 28.4 + - - +
818A THR* 2.8 54.7 + - - +
820A GLN* 1.3 92.2 - - - +
822A LEU* 1.3 67.7 + - + +
824A PRO* 4.8 1.4 - - - +
825A VAL* 3.5 17.3 - - - +
847A LYS* 3.8 13.5 - - - +
851A GLU* 2.4 32.3 + - - -
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Residues in contact with LEU 822 (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 THR* 2.8 34.9 + - + +
819A VAL* 4.2 0.9 - - - +
821A ARG* 1.3 102.1 - - + +
823A LEU* 1.3 67.6 + - - +
824A PRO 2.9 3.9 - - - -
825A VAL* 3.0 15.1 + - + -
826A LEU* 2.6 43.0 + - + +
850A LEU* 5.1 5.8 - - + -
851A GLU* 5.0 7.9 - - + -
854A GLN* 3.4 48.5 - - + +
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Residues in contact with LEU 823 (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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797A GLY 6.0 2.7 - - - +
798A LEU* 5.7 4.3 - - + -
819A VAL* 2.6 40.5 + - + +
820A GLN* 4.4 1.8 - - - +
822A LEU* 1.3 72.1 - - - +
824A PRO* 1.4 73.7 - - + +
826A LEU* 3.3 7.1 + - - +
827A CYS* 3.2 44.2 + - - -
833A THR 4.8 3.1 - - - +
834A PRO* 4.9 14.6 - - + +
837A VAL* 3.6 28.7 - - + -
838A VAL* 5.1 6.7 - - + -
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Residues in contact with PRO 824 (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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820A GLN* 3.1 19.7 - - - +
821A ARG 5.0 1.6 - - - +
822A LEU 2.9 1.1 - - - -
823A LEU* 1.4 99.0 - - + +
825A VAL* 1.3 69.1 + - + +
826A LEU 3.0 1.4 + - - -
827A CYS* 3.4 4.6 + - + +
828A GLN* 3.3 28.6 + - - +
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Residues in contact with VAL 825 (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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821A ARG 3.5 24.2 - - - +
822A LEU* 3.0 15.3 + - + +
824A PRO* 1.3 76.6 - - + +
826A LEU* 1.3 61.4 + - - +
828A GLN* 3.7 17.7 - - - +
829A ALA* 4.2 5.7 + - - +
854A GLN* 3.7 25.8 - - + +
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Residues in contact with LEU 826 (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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822A LEU* 2.6 41.0 + - + +
823A LEU 3.7 3.4 - - - +
825A VAL* 1.3 70.7 - - - +
827A CYS* 1.3 54.9 + - - +
828A GLN 2.7 15.6 + - - -
829A ALA* 3.1 21.4 + - + +
832A LEU* 4.2 27.6 + - + +
837A VAL* 3.4 32.8 - - + -
850A LEU* 3.7 25.4 - - + +
853A VAL* 4.7 7.4 - - + -
854A GLN* 4.3 33.2 - - + +
857A LEU* 5.5 2.5 - - + -
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Residues in contact with CYS 827 (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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823A LEU* 3.2 33.4 + - - +
824A PRO* 3.4 4.8 + - + +
826A LEU* 1.3 75.9 - - - +
828A GLN* 1.3 61.6 + - + +
829A ALA 3.7 6.0 - - - +
832A LEU* 4.5 15.4 - - - +
833A THR* 3.0 32.5 - - - -
834A PRO* 4.9 2.7 - - - -
837A VAL* 5.1 1.1 - - - -
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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