Contacts of the helix formed by residues 872 - 883 (chain A) in PDB entry 5M64
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 ASP 872 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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868A THR* 3.5 33.6 - - - +
869A PRO* 3.8 3.8 + - - +
870A ALA 5.3 0.3 - - - -
871A ASP* 1.3 100.6 + - - +
873A PRO* 1.3 71.7 - - + +
874A GLU* 4.3 5.4 - - + +
875A LEU* 3.2 18.9 + - + +
876A LEU* 3.0 19.9 + - - +
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Residues in contact with PRO 873 (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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871A ASP 3.4 8.3 - - - +
872A ASP* 1.3 85.8 - - + +
874A GLU* 1.3 58.0 + - - +
876A LEU* 3.0 12.2 + - + +
877A LYS* 2.9 41.2 + - + +
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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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864A LEU* 5.2 19.1 - - + +
872A ASP* 3.2 6.6 - - + -
873A PRO* 1.3 79.0 - - - +
875A LEU* 1.3 62.8 + - - +
877A LYS* 3.3 16.2 + - - +
878A ARG* 3.0 50.7 + - - +
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Residues in contact with LEU 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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858A ALA* 5.2 4.7 - - + +
859A ALA* 5.4 4.3 - - + -
862A THR* 3.7 35.7 - - + +
864A LEU* 5.1 7.4 - - + -
868A THR* 4.7 15.9 - - - +
869A PRO 4.1 18.6 - - - +
870A ALA* 4.3 13.5 - - + -
872A ASP* 3.2 21.3 + - + +
874A GLU* 1.3 79.5 - - - +
876A LEU* 1.3 60.5 + - - +
877A LYS 3.6 0.2 + - - -
878A ARG* 3.7 7.5 + - - +
879A LEU* 3.5 33.4 + - + +
974A THR* 4.7 6.5 - - + -
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Residues in contact with LEU 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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871A ASP 6.0 2.0 - - - +
872A ASP 3.0 12.5 + - - +
873A PRO* 3.0 16.9 + - + +
875A LEU* 1.3 75.6 - - - +
877A LYS* 1.3 65.2 + - + +
878A ARG 3.1 9.3 + - - -
879A LEU* 4.1 14.3 - - + +
880A GLN* 3.2 48.4 + - - +
972A TYR* 5.0 21.5 - - + -
632B SER* 6.3 0.9 - - - -
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Residues in contact with LYS 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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873A PRO* 2.9 24.6 + - + +
874A GLU* 3.3 12.2 + - - +
876A LEU* 1.3 83.4 - - + +
878A ARG* 1.3 78.0 + - - +
880A GLN* 3.4 26.5 - - - +
881A GLU* 3.4 18.7 - - - +
632B SER* 6.1 2.4 - - - -
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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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862A THR* 3.2 35.5 + - - +
864A LEU* 5.6 4.9 - - + +
874A GLU* 3.0 37.8 + - - +
875A LEU 3.7 4.5 + - - +
876A LEU 3.1 0.8 - - - -
877A LYS* 1.3 102.4 + - - +
879A LEU* 1.3 67.9 + - - +
880A GLN 3.3 1.1 - - - -
881A GLU* 3.1 14.2 + - - +
882A ILE* 3.1 23.4 + - + +
64I LYS 5.2 0.2 + - - -
65I SER* 3.4 44.0 + - - +
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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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858A ALA* 5.6 7.6 - - + -
862A THR* 5.9 0.8 - - - -
870A ALA* 6.1 0.2 - - + -
875A LEU* 3.5 40.3 + - + +
876A LEU* 4.1 11.4 - - + +
878A ARG* 1.3 79.1 - - - +
880A GLN* 1.3 75.8 + - - +
882A ILE* 3.2 30.8 - - + +
883A LEU* 3.2 21.7 - - + +
972A TYR* 3.5 41.5 - - + +
973A GLU 5.5 0.7 - - - +
974A THR* 3.7 22.9 - - + -
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Residues in contact with GLN 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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876A LEU* 3.2 30.7 - - - +
877A LYS* 3.4 41.1 - - - +
879A LEU* 1.3 81.6 - - - +
881A GLU* 1.3 79.0 + - + +
883A LEU* 3.6 14.6 - - - +
884A ARG* 3.4 19.8 - - - +
972A TYR* 3.8 21.4 + - + -
632B SER* 4.5 6.2 - - - -
633B THR* 3.4 39.1 + - + +
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Residues in contact with GLU 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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877A LYS 3.4 21.5 - - - +
878A ARG* 3.1 9.5 + - - +
880A GLN* 1.3 95.3 + - + +
882A ILE* 1.3 61.9 + - + +
883A LEU 3.4 0.9 - - - -
884A ARG* 3.8 21.4 + - - +
885A ASP* 4.5 3.8 - - - +
888A LYS* 4.8 5.0 - - - +
633B THR* 5.6 4.2 - - - -
634B ARG* 3.8 23.7 + - - -
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Residues in contact with ILE 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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858A ALA* 6.2 2.2 - - + -
861A VAL* 4.4 16.8 - - + +
862A THR* 6.1 3.1 - - - -
878A ARG* 3.3 13.9 - - + +
879A LEU* 3.2 29.4 - - + +
881A GLU* 1.3 78.6 - - + +
883A LEU* 1.3 57.1 + - + +
884A ARG 3.3 6.1 + - - -
885A ASP* 4.0 1.6 - - - +
888A LYS* 3.2 45.4 - - + +
889A SER* 3.4 13.9 + - - -
891A ILE* 6.2 1.1 - - + -
892A LEU* 3.7 26.2 - - + -
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Residues in contact with LEU 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 LEU* 3.2 23.4 + - + +
880A GLN* 3.6 17.5 - - - +
881A GLU 3.4 0.2 - - - -
882A ILE* 1.3 78.0 - - + +
884A ARG* 1.3 90.8 + - - +
885A ASP 3.5 4.4 + - - +
889A SER* 4.4 7.2 - - - +
959A VAL* 4.2 24.9 - - + +
960A MET 4.8 1.8 - - - +
963A GLY* 4.0 27.6 - - - +
972A TYR* 4.3 10.8 - - + -
633B THR* 3.9 8.1 - - + -
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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
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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