Contacts of the helix formed by residues 843 - 853 (chain A) in PDB entry 5L6P
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 SER 843 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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789A ASP* 3.4 21.3 - - - -
803A ARG* 3.8 0.2 - - - -
841A ASP 3.5 2.2 + - - -
842A MET* 1.3 76.2 - - - +
844A ASN* 1.3 65.3 + - - +
845A GLN* 3.7 7.7 + - - +
846A ASP* 2.9 47.2 + - - -
847A VAL* 3.0 13.5 + - - +
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Residues in contact with ASN 844 (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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789A ASP* 3.5 22.3 + - - +
790A PRO* 2.9 33.2 + - - +
793A THR* 4.1 11.8 + - - +
802A ILE* 3.5 31.2 - - + +
803A ARG* 3.0 34.9 + - - +
843A SER* 1.3 72.7 - - - +
845A GLN* 1.3 61.1 + - - +
847A VAL* 3.3 14.9 + - - +
848A ILE* 3.4 13.9 + - + +
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Residues in contact with GLN 845 (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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843A SER* 3.2 7.5 + - - +
844A ASN* 1.3 74.3 - - - +
846A ASP* 1.4 65.7 - - - +
848A ILE* 3.5 25.5 + - - +
849A ASN* 3.2 45.8 + - - +
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Residues in contact with ASP 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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842A MET* 3.3 18.1 - - + +
843A SER* 2.9 42.6 + - - +
845A GLN* 1.4 76.0 - - - +
847A VAL* 1.4 56.9 + - - +
849A ASN* 3.8 9.9 + - - +
850A ALA* 2.9 34.7 + - - +
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Residues in contact with VAL 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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802A ILE* 4.3 15.3 - - + +
803A ARG* 3.8 23.6 - - + +
839A TYR* 3.6 47.6 - - + -
842A MET* 3.2 19.7 - - + -
843A SER 3.0 17.6 + - - +
844A ASN* 3.5 8.7 - - - +
845A GLN 3.3 0.4 - - - -
846A ASP* 1.4 73.2 - - - +
848A ILE* 1.3 59.7 + - - +
850A ALA* 3.3 1.7 + - - +
851A VAL* 2.9 40.2 + - + +
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Residues in contact with ILE 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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802A ILE* 3.7 36.6 - - + -
807A PRO* 6.0 0.4 - - + +
810A ILE* 4.1 25.6 - - + -
844A ASN* 3.4 15.8 + - + +
845A GLN* 3.8 31.2 - - - +
847A VAL* 1.3 74.4 - - + +
849A ASN* 1.4 63.9 + - - +
851A VAL* 3.6 6.8 + - - +
852A GLU* 3.2 49.6 + - + +
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Residues in contact with ASN 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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845A GLN* 3.2 43.5 + - - +
846A ASP* 3.8 11.2 + - - +
848A ILE* 1.4 73.5 - - - +
850A ALA* 1.4 63.8 + - - +
852A GLU* 3.4 18.7 + - - +
853A GLN* 3.2 30.9 + - + +
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Residues in contact with ALA 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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842A MET* 3.7 17.7 - - + -
846A ASP 2.9 18.9 + - - +
847A VAL 3.3 3.8 + - - +
849A ASN* 1.4 73.4 - - - +
851A VAL* 1.4 60.2 + - + +
853A GLN* 3.1 15.5 + - - +
854A ASP 3.3 0.3 + - - -
855A TYR* 2.9 46.4 + - + +
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Residues in contact with VAL 851 (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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807A PRO* 3.8 24.5 - - + -
822A TRP* 3.7 33.0 - - + -
839A TYR* 3.9 25.4 - - + +
847A VAL* 2.9 28.8 + - + +
848A ILE* 3.8 6.3 - - - +
850A ALA* 1.4 74.9 - - + +
852A GLU* 1.4 55.2 + - - +
854A ASP* 3.1 11.8 + - - +
855A TYR 3.8 14.4 - - - +
856A ARG* 3.1 23.2 + - - +
877A ARG* 5.2 4.1 - - - -
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Residues in contact with GLU 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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807A PRO* 5.5 8.6 - - + +
811A ALA* 5.8 3.8 - - - +
848A ILE* 3.2 34.5 + - - +
849A ASN* 3.5 24.0 - - - +
850A ALA 3.3 0.2 - - - -
851A VAL* 1.4 74.9 - - - +
853A GLN* 1.3 65.9 + - - +
854A ASP* 3.2 9.9 + - - +
877A ARG* 4.4 24.0 + - - +
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Residues in contact with GLN 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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849A ASN* 3.2 16.4 + - + +
850A ALA* 3.1 11.2 + - - +
852A GLU* 1.3 81.6 - - - +
854A ASP* 1.4 70.2 + - - +
855A TYR* 3.4 4.1 + - + +
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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