Contacts of the helix formed by residues 850 - 858 (chain A) in PDB entry 6CIM
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 850 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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798A ILE* 4.5 9.6 - - - +
844A LYS* 5.5 1.0 + - - -
846A ILE* 4.1 8.3 - - + +
848A ARG* 3.6 14.5 + - - +
849A MET* 1.3 95.2 - - - +
851A GLY* 1.3 75.1 + - - +
852A ASN* 2.6 34.1 + - - +
853A PHE* 3.1 23.7 - - - +
854A ALA* 3.5 9.9 + - - +
17L C 5.9 0.2 - - - -
18L A 3.1 37.0 + - - +
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Residues in contact with GLY 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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794A LEU* 3.8 27.9 - - - +
797A ASP* 5.5 0.3 - - - +
798A ILE* 4.3 8.1 - - - +
850A ASN* 1.3 82.9 - - - +
852A ASN* 1.3 57.0 + - - -
854A ALA* 3.1 8.7 - - - +
855A ARG* 2.9 31.5 + - - +
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Residues in contact with ASN 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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844A LYS* 5.4 6.9 + - - +
850A ASN* 2.6 32.4 + - - +
851A GLY* 1.3 71.9 - - - +
853A PHE* 1.3 67.0 + - - +
855A ARG* 3.6 15.9 - - + +
856A LYS* 2.9 50.8 + - + +
18L A 3.4 20.9 + - - -
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Residues in contact with PHE 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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805A TYR* 3.8 27.6 - + - -
834A ASP* 6.1 0.4 - - - -
837A LEU* 5.0 11.2 - - + -
843A LEU* 5.3 11.4 - - + +
844A LYS* 4.0 21.5 - - + -
845A PRO* 5.1 1.6 - - + -
846A ILE* 3.2 41.7 - - + -
849A MET* 3.6 24.2 - - + -
850A ASN* 3.1 19.5 - - - +
852A ASN* 1.3 83.5 + - - +
854A ALA* 1.3 55.1 + - - +
856A LYS* 3.8 4.5 - - - +
857A LEU* 2.9 67.1 + - + +
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Residues in contact with ALA 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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797A ASP* 3.7 22.0 - - + +
798A ILE* 4.2 5.8 - - - -
801A ALA* 3.4 31.0 - - + -
849A MET* 5.0 1.3 - - + -
850A ASN 3.5 10.0 + - - +
851A GLY* 3.1 12.4 + - - +
853A PHE* 1.3 81.6 - - - +
855A ARG* 1.3 62.8 + - - +
857A LEU* 3.2 1.0 + - - -
858A MET* 3.0 31.5 + - - +
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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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794A LEU* 5.8 5.6 - - + -
797A ASP* 4.2 21.1 + - + +
851A GLY 2.9 20.7 + - - +
852A ASN* 3.3 18.9 + - + +
854A ALA* 1.3 76.9 - - - +
856A LYS* 1.3 63.4 + - + +
857A LEU 3.6 0.2 + - - -
858A MET* 3.8 9.3 + - - +
859A THR* 4.0 7.6 + - - -
886A TYR* 5.8 0.2 - - - -
890A LYS* 4.7 15.2 + - - +
894A ARG* 2.8 54.8 - - - +
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Residues in contact with LYS 856 (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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841A MET* 4.9 3.3 - - - +
842A ASN 5.9 0.4 + - - -
843A LEU* 3.9 33.1 - - + +
852A ASN* 2.9 35.9 + - + +
853A PHE* 4.1 4.5 - - - +
855A ARG* 1.3 79.1 - - + +
857A LEU* 1.3 61.2 + - - +
858A MET 3.5 0.2 - - - -
859A THR* 3.4 12.3 + - - -
862A THR* 3.6 11.1 - - - +
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Residues in contact with LEU 857 (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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801A ALA* 4.5 2.9 - - + +
805A TYR* 4.0 24.5 - - + -
808A PHE* 3.9 19.3 - - + -
837A LEU* 4.1 22.7 - - + -
843A LEU* 4.4 7.2 - - + -
853A PHE* 2.9 50.3 + - + +
854A ALA* 3.2 2.4 + - - +
856A LYS* 1.3 74.8 - - - +
858A MET* 1.3 77.5 + - + +
859A THR 3.2 4.3 - - - -
862A THR* 2.6 42.7 + - + -
883A MET* 4.1 1.7 - - - +
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Residues in contact with MET 858 (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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797A ASP 4.7 1.3 - - - +
800A ASN 4.1 1.3 - - - -
801A ALA* 3.5 35.4 - - + -
804A PHE* 3.4 40.8 - - + -
808A PHE* 4.9 0.4 - - + -
854A ALA 3.0 20.2 + - - +
855A ARG* 3.8 7.4 + - - +
856A LYS 3.5 0.6 - - - -
857A LEU* 1.3 95.9 - - + +
859A THR* 1.3 62.8 + - - +
883A MET* 4.0 15.7 - - + -
886A TYR* 3.5 41.1 - - + +
887A LEU* 3.9 14.6 - - - +
890A LYS* 4.9 4.7 + - - +
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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