Contacts of the helix formed by residues 879 - 898 (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 879 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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845A GLY* 4.6 4.2 - - - +
877A ASN* 3.2 1.2 + - - -
878A ILE* 1.3 82.9 - - - +
880A GLY* 1.3 70.3 - - - +
881A LYS 3.5 1.8 - - - -
882A GLN* 3.2 9.7 + - - +
883A ALA* 3.0 18.8 + - - +
914A GLY 5.8 0.5 + - - -
17B T 3.8 26.6 + - - -
18B A 3.8 15.3 + - - -
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Residues in contact with GLY 880 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
845A GLY 5.3 1.8 + - - -
849A ALA* 4.4 11.1 - - - +
874A ILE 4.3 0.7 - - - -
875A ALA* 4.2 20.9 - - - -
877A ASN 3.2 14.1 + - - -
879A GLY* 1.3 70.3 - - - +
881A LYS* 1.3 58.2 - - - +
883A ALA* 2.4 34.1 + - - -
884A LEU* 2.7 16.1 + - - -
17B T 4.9 0.8 + - - -
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Residues in contact with LYS 881 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
848A GLN* 3.3 43.2 - - + +
849A ALA* 3.9 9.3 - - - +
852A THR* 3.3 28.2 - - + +
855A ARG* 6.2 1.3 - - - +
880A GLY* 1.3 71.8 - - - +
882A GLN* 1.3 74.0 + - - +
885A GLU* 3.1 50.6 + - + +
17B T 3.4 16.6 + - - +
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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
----------------------------------------------------------
879A GLY 3.5 10.5 - - - +
880A GLY 2.6 4.0 + - - -
881A LYS* 1.3 95.9 + - - +
883A ALA* 1.3 59.6 + - - +
884A LEU 3.5 0.2 - - - -
885A GLU* 4.5 8.3 + - - -
886A THR* 2.9 35.8 + - - -
915A LYS* 3.8 40.2 - - + +
17B T 3.5 45.7 + - - +
18B A 4.1 3.8 - - - +
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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
----------------------------------------------------------
874A ILE* 3.6 29.2 - - + +
877A ASN* 6.2 0.7 - - + -
878A ILE 5.8 0.2 - - - +
879A GLY 3.0 12.7 + - - +
880A GLY* 2.4 16.8 + - - +
882A GLN* 1.3 66.0 - - - +
884A LEU* 1.3 65.7 + - - +
886A THR* 4.9 1.1 - - - -
887A VAL* 3.1 26.0 + - - +
909A ALA* 3.7 13.4 - - - +
911A ASN 5.6 1.3 - - - +
914A GLY* 4.4 11.0 - - - +
915A LYS 4.4 8.2 - - - +
918A LEU* 4.9 0.4 - - - +
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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
----------------------------------------------------------
849A ALA 3.9 3.1 - - - +
852A THR* 3.3 49.6 - - + +
853A VAL* 3.4 13.9 - - + +
856A LEU* 4.9 6.7 - - + -
860A LEU* 4.7 1.2 - - + +
871A VAL* 4.2 14.1 - - + +
874A ILE* 3.7 23.8 - - + -
875A ALA* 3.6 31.9 - - + -
880A GLY 2.7 18.6 + - - +
883A ALA* 1.3 69.0 - - - +
885A GLU* 1.3 67.5 + - - +
887A VAL* 2.9 20.0 + - + +
888A GLN* 2.9 12.9 + - - +
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Residues in contact with GLU 885 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
852A THR* 4.2 7.1 - - + +
855A ARG* 3.9 16.8 + - - +
856A LEU* 4.3 19.9 - - + +
881A LYS* 3.1 39.6 + - + +
882A GLN* 4.1 10.0 + - - +
884A LEU* 1.3 76.6 - - - +
886A THR* 1.3 59.1 + - - +
888A GLN* 2.7 27.0 + - - +
889A ARG* 3.0 13.1 + - - +
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Residues in contact with THR 886 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
882A GLN* 2.9 25.3 + - - -
883A ALA 4.6 0.2 - - - -
885A GLU* 1.3 73.8 - - - +
887A VAL* 1.3 65.6 + - - +
888A GLN 3.0 0.2 + - - -
889A ARG* 3.1 5.3 + - - +
890A LEU* 2.9 34.0 + - + +
915A LYS* 3.5 25.8 - - - +
918A LEU* 3.6 32.8 - - + -
919A GLU* 4.0 22.2 + - + +
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Residues in contact with VAL 887 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
860A LEU* 3.2 26.9 - - + -
864A HIS* 5.0 4.7 - - - +
866A LEU* 5.3 1.1 - - + -
874A ILE* 3.8 20.2 - - + -
883A ALA 3.1 17.6 + - - +
884A LEU* 2.9 8.3 + - + +
886A THR* 1.3 79.0 - - - +
888A GLN* 1.3 60.7 + - - +
890A LEU* 5.4 0.2 - - - -
891A LEU* 3.1 35.0 + - + +
905A VAL* 4.5 14.4 - - + -
906A VAL* 5.6 1.1 - - + -
909A ALA* 3.4 33.4 - - + -
918A LEU* 4.1 8.2 - - + +
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Residues in contact with GLN 888 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
856A LEU* 4.2 23.8 - - + +
859A VAL* 4.1 25.4 - - + +
860A LEU* 3.5 22.0 - - + -
884A LEU 2.9 7.3 + - - +
885A GLU* 2.7 21.5 + - - +
887A VAL* 1.3 74.2 - - - +
889A ARG* 1.3 73.6 + - - +
890A LEU 3.4 0.7 + - - -
891A LEU* 4.4 0.6 - - - +
892A PRO* 3.8 15.9 - - - +
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Residues in contact with ARG 889 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
885A GLU 3.0 13.4 + - - +
886A THR* 4.3 5.4 - - - +
888A GLN* 1.3 89.5 - - - +
890A LEU* 1.3 61.9 + - + +
891A LEU 3.7 0.2 - - - -
892A PRO* 4.9 6.8 - - - +
893A VAL* 5.7 2.8 - - - +
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Residues in contact with LEU 890 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
886A THR* 2.9 29.2 + - + +
887A VAL* 4.0 0.9 - - - -
889A ARG* 1.3 81.9 - - + +
891A LEU* 1.3 66.0 + - - +
892A PRO 3.5 1.8 - - - -
893A VAL* 3.9 13.5 + - + +
894A LEU* 3.2 37.6 + - + +
918A LEU* 4.9 12.3 - - + -
919A GLU* 5.2 14.6 - - + +
922A GLN* 3.7 43.3 - - + +
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Residues in contact with LEU 891 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
860A LEU* 5.1 7.6 - - + -
863A ALA* 4.5 9.2 - - + +
864A HIS* 3.4 49.1 - - + +
887A VAL* 3.1 23.2 + - + +
888A GLN* 4.4 1.8 - - - +
890A LEU* 1.3 77.1 - - - +
892A PRO* 1.4 80.3 - - + +
893A VAL 3.4 0.2 + - - -
894A LEU* 3.4 9.6 + - - +
895A CYS* 3.5 33.3 + - - -
901A THR 5.0 0.4 - - - +
902A LEU* 5.4 3.4 - - + -
905A VAL* 3.6 31.9 - - + -
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Residues in contact with PRO 892 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
863A ALA* 5.6 10.5 - - + +
888A GLN 3.8 12.8 - - - +
889A ARG 4.9 5.8 - - - +
890A LEU 4.9 0.9 - - - -
891A LEU* 1.4 97.0 - - + +
893A VAL* 1.3 66.8 + - + +
895A CYS* 4.2 1.3 - - + +
896A GLN* 3.1 48.3 + - + +
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Residues in contact with VAL 893 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
889A ARG 5.7 3.1 - - - +
890A LEU* 3.9 15.8 + - + +
891A LEU 3.4 0.8 - - - -
892A PRO* 1.3 82.1 - - + +
894A LEU* 1.3 58.8 + - + +
896A GLN* 5.0 1.3 - - - -
897A ASP* 2.8 40.1 + - + +
898A HIS* 3.8 21.1 - - + -
922A GLN* 4.3 22.0 - - + +
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Residues in contact with LEU 894 (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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890A LEU* 3.2 44.0 - - + +
891A LEU* 3.4 5.5 + - - +
892A PRO 3.3 0.6 + - - -
893A VAL* 1.3 73.7 - - - +
895A CYS* 1.3 54.3 + - - +
898A HIS* 2.7 42.0 + - + +
899A GLY 2.7 13.8 + - - -
900A LEU* 4.0 24.5 - - + -
905A VAL* 3.3 27.4 - - + -
918A LEU* 4.3 11.7 - - + -
921A VAL* 3.9 18.2 - - + -
922A GLN* 3.8 19.1 - - + -
925A LEU* 5.4 0.9 - - + -
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Residues in contact with CYS 895 (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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864A HIS* 6.3 0.9 - - - -
891A LEU* 3.5 39.9 + - - +
892A PRO* 4.2 2.2 - - + +
894A LEU* 1.3 79.1 - - - +
896A GLN* 1.3 61.8 + - + +
899A GLY* 3.2 19.1 - - - +
900A LEU 3.0 23.3 + - - +
901A THR 3.5 13.2 - - - -
902A LEU* 4.8 2.0 - - - -
905A VAL* 4.5 1.6 - - - -
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Residues in contact with GLN 896 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
892A PRO* 3.1 38.3 + - + +
893A VAL* 4.2 1.1 - - - +
895A CYS* 1.3 80.9 - - + +
897A ASP* 1.3 63.9 + - - +
899A GLY* 4.5 1.0 + - - -
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Residues in contact with ASP 897 (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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893A VAL* 2.8 23.9 + - + +
896A GLN* 1.3 76.6 - - - +
898A HIS* 1.3 87.0 + - + +
899A GLY* 3.3 0.9 + - - -
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Residues in contact with HIS 898 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
893A VAL* 3.8 23.0 + - + -
894A LEU* 2.7 32.8 + - + +
897A ASP* 1.3 91.6 + - - +
899A GLY* 1.3 54.3 + - - -
900A LEU* 2.9 8.8 + - + +
922A GLN* 4.6 15.2 + - + -
925A LEU* 3.8 28.5 - - + -
926A PRO* 3.5 39.6 - - + +
936A GLN* 2.4 35.9 + - - +
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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
------------------------------------------------------------
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