Contacts of the helix formed by residues 874 - 886 (chain A) in PDB entry 1M8X
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 THR 874 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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873A ALA* 1.3 74.3 - - - +
875A PRO* 1.3 82.2 - - - +
876A ALA* 3.4 12.4 + - + +
877A GLU* 2.8 50.2 + - + +
878A ARG* 2.9 23.1 + - - +
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Residues in contact with PRO 875 (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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874A THR* 1.3 90.5 - - - +
876A ALA* 1.3 55.3 + - - +
878A ARG* 3.7 24.0 - - + +
879A GLN* 3.0 29.5 + - - +
913A GLN* 4.9 2.1 + - - -
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Residues in contact with ALA 876 (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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874A THR* 3.0 13.4 + - + +
875A PRO* 1.3 78.1 - - - +
877A GLU* 1.3 65.8 - - + +
879A GLN* 3.2 6.4 + - - +
880A LEU* 3.0 23.6 + - - +
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Residues in contact with GLU 877 (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 GLN* 5.2 6.2 + - - +
846A LEU* 3.8 32.9 + - + +
847A ARG* 4.3 32.6 + - + -
873A ALA* 3.6 11.3 - - + -
874A THR* 2.8 44.2 + - + +
876A ALA* 1.3 80.5 - - + +
878A ARG* 1.3 61.3 + - - +
880A LEU* 3.4 10.5 + - - +
881A VAL* 3.1 27.9 + - - +
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Residues in contact with ARG 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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870A LEU* 3.2 51.7 + - + +
871A GLU 4.0 9.5 + - - -
873A ALA* 2.7 31.2 + - + -
874A THR 2.9 11.4 + - - +
875A PRO* 3.7 28.2 - - + +
876A ALA 3.2 0.2 - - - -
877A GLU* 1.3 75.4 - - - +
879A GLN* 1.3 54.0 + - - +
881A VAL 3.3 0.7 + - - -
882A PHE* 2.8 33.4 + - - +
905A PHE* 3.4 14.1 - - + -
908A PHE* 3.2 34.8 + - - +
909A GLY* 4.9 6.3 - - - -
913A GLN* 4.2 7.6 - - - +
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Residues in contact with GLN 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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875A PRO 3.0 16.8 + - - +
876A ALA* 3.2 7.4 + - - +
878A ARG* 1.3 73.6 - - - +
880A LEU* 1.3 61.7 + - - +
882A PHE* 4.0 11.7 - - - -
883A ASN* 2.6 69.9 + - - +
913A GLN* 3.1 28.9 + - - +
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Residues in contact with LEU 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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846A LEU* 5.0 6.3 - - + +
847A ARG* 4.3 31.0 - - + +
850A ALA* 4.0 32.5 - - + +
853A ILE* 4.7 7.0 - - + -
876A ALA 3.0 12.2 + - - +
877A GLU* 3.5 12.1 - - - +
879A GLN* 1.3 79.4 - - - +
881A VAL* 1.3 66.5 + - + +
883A ASN* 3.7 18.1 + - - +
884A GLU* 3.9 14.7 + - - +
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Residues in contact with VAL 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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846A LEU* 3.8 29.4 - - + -
853A ILE* 3.8 34.2 - - + +
866A ILE* 4.5 11.4 - - + -
870A LEU* 4.1 14.1 - - + -
877A GLU 3.1 15.5 + - - +
878A ARG 3.6 7.2 - - - +
879A GLN 3.1 0.4 - - - -
880A LEU* 1.3 78.4 - - + +
882A PHE* 1.3 66.5 + - - +
884A GLU* 3.3 10.7 + - - -
885A ILE* 3.5 14.2 - - + +
901A VAL* 4.8 1.3 - - + -
905A PHE* 3.8 22.7 - - + -
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Residues in contact with PHE 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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878A ARG 2.8 17.9 + - - +
879A GLN* 3.1 24.7 + - - +
881A VAL* 1.3 75.9 - - - +
883A ASN* 1.3 65.4 + - - +
885A ILE* 3.0 21.3 + - + +
886A LEU* 3.1 53.7 + - + +
905A PHE* 3.7 21.3 - + + -
913A GLN* 3.7 44.2 - - + +
916A ALA* 3.7 10.1 - - + -
917A LEU* 3.7 28.9 - - + -
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Residues in contact with ASN 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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879A GLN* 2.6 56.7 + - - +
880A LEU* 3.9 9.9 - - - +
881A VAL 3.3 0.4 - - - -
882A PHE* 1.3 75.3 - - - +
884A GLU* 1.3 63.4 + - + +
885A ILE 3.7 0.2 + - - -
886A LEU* 4.3 10.2 + - - +
887A GLN* 5.1 2.4 + - - +
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Residues in contact with GLU 884 (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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850A ALA* 3.7 8.3 - - - +
851A GLY* 2.7 42.3 + - - -
853A ILE* 3.0 42.1 + - + +
854A MET* 3.2 23.5 + - + +
880A LEU* 3.9 9.9 + - - +
881A VAL 3.3 2.4 + - - +
882A PHE 3.1 1.2 - - - -
883A ASN* 1.3 82.9 - - + +
885A ILE* 1.3 60.1 + - - +
886A LEU 3.7 0.4 - - - -
887A GLN* 5.3 2.6 + - - +
888A ALA* 5.2 2.8 + - - +
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Residues in contact with ILE 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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853A ILE* 3.4 31.9 - - + -
854A MET* 3.9 8.3 - - - -
857A SER* 4.4 1.6 - - - +
881A VAL* 3.5 6.3 - - + +
882A PHE* 3.0 21.3 + - + +
884A GLU* 1.3 79.3 - - - +
886A LEU* 1.3 64.9 + - - +
887A GLN 3.5 1.1 - - - -
888A ALA 3.5 2.0 - - - -
889A ALA* 2.9 31.4 + - - +
892A LEU* 3.8 21.8 - - + -
901A VAL* 4.6 5.6 - - + -
902A ILE* 3.9 19.7 - - + -
905A PHE* 3.4 39.9 - - + -
917A LEU* 5.2 1.1 - - + -
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Residues in contact with LEU 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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882A PHE* 3.1 50.7 + - + +
883A ASN* 4.6 6.3 - - - +
884A GLU 3.7 0.6 - - - -
885A ILE* 1.3 77.9 - - - +
887A GLN* 1.3 69.3 + - - +
889A ALA* 3.1 20.0 + - - +
916A ALA* 3.8 16.8 - - + +
917A LEU* 4.9 1.8 - - + -
919A GLU* 5.9 0.2 - - + -
920A ARG* 3.3 39.7 + - + +
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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