Contacts of the helix formed by residues 845 - 855 (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 845 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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843A ASN* 3.2 4.9 + - - +
844A GLY* 1.3 70.5 - - - +
846A GLY* 1.3 49.6 + - - -
847A LYS 3.7 1.1 - - - -
848A GLN* 3.1 7.9 + - - +
849A ALA* 2.6 38.9 + - - +
877A ASN 5.8 0.2 + - - -
878A ILE* 5.0 0.8 - - - +
879A GLY 4.6 11.4 - - - +
880A GLY 5.3 0.8 + - - -
881A LYS 5.2 0.7 + - - -
16B G 4.0 11.3 - - - +
17B T 3.0 30.7 + - - +
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Residues in contact with GLY 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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811A GLY* 5.1 4.0 - - - -
815A ALA* 5.6 3.4 - - - -
840A ILE* 4.8 1.1 - - - +
841A ALA* 4.7 16.2 - - - -
843A ASN 3.0 11.4 + - - -
844A GLY 2.5 15.5 + - - -
845A GLY* 1.3 67.0 - - - +
847A LYS* 1.3 69.1 + - - +
849A ALA* 2.7 18.1 + - - +
850A LEU* 2.8 22.5 + - - +
16B G 4.8 1.0 + - - -
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Residues in contact with LYS 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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811A GLY* 5.8 1.2 - - - -
814A GLN* 3.2 53.3 + - + +
815A ALA* 4.9 4.2 - - - +
818A THR* 3.2 30.1 - - - +
821A ARG* 3.8 15.6 - - - +
846A GLY* 1.3 72.5 - - - +
848A GLN* 1.3 72.1 + - - +
850A LEU* 4.4 1.9 - - - +
851A GLU* 3.2 41.8 + - - +
16B G 3.7 15.4 + - - +
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Residues in contact with GLN 848 (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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845A GLY 3.1 12.2 + - - +
846A GLY 3.0 1.0 - - - -
847A LYS* 1.3 89.8 + - - +
849A ALA* 1.3 58.6 + - - +
851A GLU* 3.9 14.7 + - - +
852A THR* 2.8 32.7 + - - -
881A LYS* 3.3 26.0 - - + +
16B G 2.7 44.2 + - - +
17B T 3.1 28.0 - - - +
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Residues in contact with ALA 849 (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 ILE* 4.0 14.8 - - + +
845A GLY 2.6 17.7 + - - +
846A GLY 2.7 10.8 + - - +
848A GLN* 1.3 69.8 - - - +
850A LEU* 1.4 51.5 - - - +
852A THR* 2.8 24.4 + - - -
853A VAL* 2.8 19.5 + - - +
875A ALA* 3.9 23.3 - - + +
877A ASN 5.3 0.9 - - - +
880A GLY* 4.4 10.8 - - - +
881A LYS 3.9 11.4 - - - +
884A LEU* 3.9 1.7 - - - +
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Residues in contact with LEU 850 (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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815A ALA* 4.4 2.7 - - - +
818A THR* 3.7 32.1 - - + +
819A VAL* 4.3 13.7 - - + +
822A LEU* 5.1 4.3 - - + -
826A LEU* 3.7 30.5 - - + +
837A VAL* 3.7 18.2 - - + +
840A ILE* 3.6 22.4 - - + +
841A ALA* 4.2 15.9 - - + -
846A GLY 2.8 23.3 + - - +
847A LYS 4.0 2.0 - - - +
849A ALA* 1.4 67.4 - - - +
851A GLU* 1.3 51.8 + - - +
852A THR 2.7 5.1 + - - -
853A VAL* 2.6 33.6 + - + +
854A GLN* 2.7 17.1 + - - +
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Residues in contact with GLU 851 (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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818A THR* 4.0 12.3 - - + -
821A ARG* 2.4 35.8 + - - -
822A LEU* 5.0 7.2 - - + +
847A LYS* 3.2 34.2 + - - +
848A GLN* 4.0 10.5 + - - +
850A LEU* 1.3 75.8 - - - +
852A THR* 1.3 59.0 + - - +
854A GLN* 4.2 13.4 - - - +
855A ARG* 3.3 29.3 + - - +
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Residues in contact with THR 852 (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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848A GLN 2.8 21.5 + - - -
849A ALA 2.8 9.0 + - - -
850A LEU 2.7 1.8 + - - -
851A GLU* 1.3 75.0 + - - +
853A VAL* 1.3 64.7 + - - +
854A GLN 3.3 0.2 - - - -
855A ARG* 3.9 12.4 + - - +
856A LEU* 3.2 31.1 + - + +
881A LYS* 3.3 33.0 - - - +
884A LEU* 3.3 32.4 - - + +
885A GLU* 4.2 8.7 - - + +
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Residues in contact with VAL 853 (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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826A LEU* 4.7 7.9 - - + -
832A LEU* 4.9 7.9 - - + -
840A ILE* 4.3 15.5 - - + -
849A ALA 2.8 13.2 + - - +
850A LEU* 2.6 29.1 + - + +
852A THR* 1.3 72.2 - - - +
854A GLN* 1.3 59.9 + - - +
857A LEU* 2.4 57.2 + - + +
871A VAL* 3.5 32.3 - - + -
872A VAL* 5.2 3.4 - - + -
875A ALA* 4.6 6.1 - - + -
884A LEU* 3.5 11.7 - - + -
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Residues in contact with GLN 854 (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* 3.4 36.6 - - + +
825A VAL* 3.7 21.7 - - + +
826A LEU* 4.3 15.7 - - + +
850A LEU 2.7 13.7 + - - +
851A GLU* 4.2 10.4 - - - +
853A VAL* 1.3 80.7 - - - +
855A ARG* 1.3 69.0 + - - +
856A LEU 3.1 0.3 + - - -
857A LEU* 3.9 4.5 + - - -
858A PRO* 4.5 7.8 - - - +
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Residues in contact with ARG 855 (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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851A GLU 3.3 19.5 + - - +
852A THR* 4.6 12.3 + - - +
854A GLN* 1.3 86.5 + - - +
856A LEU* 1.3 103.2 + - - +
858A PRO* 5.7 0.9 - - - -
859A VAL* 4.4 5.7 - - - +
881A LYS* 6.2 1.4 - - - +
885A GLU* 3.9 21.0 + - - +
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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