Contacts of the helix formed by residues 872 - 876 (chain M) in PDB entry 5D4D
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 ASN 872 (chain M).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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676M ILE* 4.2 1.8 - - - +
678M PRO* 4.4 3.8 - - - +
683M ASN* 3.3 43.4 + - - +
684M PHE* 4.3 0.2 - - - +
685M GLU 4.9 1.0 - - - +
686M ASP* 5.6 3.4 - - - +
687M ALA 5.3 1.2 + - - +
845M ASN* 5.4 4.2 + - - -
871M LEU* 1.3 73.9 - - - +
873M PRO* 1.3 74.6 - - - +
874M LEU* 2.7 40.4 + - - +
875M GLY* 3.2 14.0 + - - +
876M VAL* 4.4 3.1 + - - +
784N ASP* 2.3 41.8 + - - +
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Residues in contact with PRO 873 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
676M ILE* 3.6 16.4 - - + -
677M MET* 3.5 24.5 - - - +
678M PRO* 3.6 4.7 - - + -
871M LEU 3.6 4.2 - - - +
872M ASN* 1.3 84.5 - - - +
874M LEU* 1.3 62.3 + - + +
875M GLY 3.0 5.8 - - - -
876M VAL* 3.1 19.2 + - + +
877M PRO* 3.1 10.6 - - - +
947N ILE* 3.8 34.1 - - + +
948N THR* 4.0 7.2 - - - -
949N ILE* 3.6 25.1 - - + +
1023N MET* 4.3 2.4 - - - +
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Residues in contact with LEU 874 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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872M ASN* 2.7 21.3 + - - +
873M PRO* 1.3 72.9 - - + +
875M GLY* 1.3 60.6 + - - +
876M VAL 3.3 0.2 - - - -
877M PRO* 3.3 8.3 - - - +
878M SER* 5.0 0.7 + - - -
783N ARG* 3.6 11.4 - - + -
784N ASP* 3.1 52.5 - - - +
787N LEU* 4.1 13.7 - - + -
1023N MET* 3.4 31.0 - - + -
1028N ALA* 4.0 11.2 - - + -
1029N ARG* 3.2 46.0 + - + +
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Residues in contact with GLY 875 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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686M ASP* 4.3 7.2 - - - -
845M ASN* 5.6 7.2 - - - -
872M ASN* 3.2 12.6 + - - +
873M PRO 3.0 1.4 - - - -
874M LEU* 1.3 79.8 - - - +
876M VAL* 1.3 58.0 + - - +
878M SER 5.2 0.2 - - - -
879M ARG* 3.1 51.1 + - - +
881M ASN* 4.5 0.7 + - - +
884M GLN* 5.2 2.9 + - - -
1029N ARG* 5.4 1.1 - - - -
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Residues in contact with VAL 876 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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676M ILE* 5.2 4.3 - - + -
845M ASN* 5.5 2.2 - - - +
872M ASN 4.8 2.0 - - - +
873M PRO* 3.1 20.3 + - + +
875M GLY* 1.3 78.5 - - - +
877M PRO* 1.3 70.6 - - + +
878M SER 3.5 0.2 - - - -
879M ARG* 3.1 4.2 + - - +
880M MET* 2.9 20.5 + - - -
881M ASN* 3.8 13.3 - - - +
882M LEU* 3.7 29.6 - - + -
884M GLN* 4.0 17.3 - - - +
885M ILE* 4.2 17.9 - - + -
949N ILE* 4.2 21.1 - - + -
1020N LEU* 5.8 1.1 - - + -
1038N LEU* 5.8 0.7 - - + -
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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