Contacts of the helix formed by residues 851 - 860 (chain A) in PDB entry 3CMM
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 851 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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835A THR* 4.0 2.5 - - - -
850A ALA* 1.3 77.9 - - - +
852A ARG* 1.3 62.5 + - - +
853A GLN* 3.2 28.7 + - - +
854A LYS* 2.7 39.8 + - - +
855A THR* 3.2 18.2 + - - -
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Residues in contact with ARG 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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725A ASN* 5.8 0.4 + - - -
729A HIS* 4.0 23.8 + - - +
826A ASP* 4.8 18.8 + - - +
831A ILE* 3.7 17.0 - - + +
832A GLU* 3.4 45.2 + - - +
835A THR* 3.3 29.8 + - + +
851A ASP* 1.3 76.2 - - - +
853A GLN* 1.3 73.2 + - - +
854A LYS 3.4 0.2 - - - -
856A LYS* 3.0 28.8 + - - +
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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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16A GLU* 2.6 42.8 - - + +
23A LEU* 6.3 0.7 - - + -
24A TYR* 2.7 38.2 + - + +
851A ASP* 3.2 35.2 + - - +
852A ARG* 1.3 98.2 - - - +
854A LYS* 1.3 60.0 + - - +
856A LYS* 3.5 7.2 + - + +
857A PHE 3.2 8.8 + - - -
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Residues in contact with LYS 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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24A TYR* 4.8 3.1 - - + -
180A GLU* 6.2 3.0 - - - +
609A ILE* 4.0 15.9 - - + -
613A ILE* 5.5 0.2 - - + -
850A ALA* 3.7 23.1 - - + -
851A ASP* 2.7 25.0 + - - +
853A GLN* 1.3 71.1 - - - +
855A THR* 1.3 64.5 + - - +
857A PHE* 3.5 11.8 + - + +
858A ILE* 3.3 45.2 + - + +
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Residues in contact with THR 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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613A ILE* 3.9 24.4 - - + +
831A ILE* 4.9 2.9 - - + +
834A ILE* 3.6 31.9 - - + +
835A THR* 3.4 37.2 + - - +
838A SER* 5.3 0.7 - - - -
839A ASN* 5.1 1.4 + - - -
850A ALA* 4.1 10.7 + - - +
851A ASP 3.2 15.0 + - - -
852A ARG 3.9 0.7 - - - -
853A GLN 3.3 0.2 - - - -
854A LYS* 1.3 74.2 - - - +
856A LYS* 1.3 57.9 + - - +
858A ILE* 3.1 1.6 + - - +
859A ALA* 2.8 34.9 + - + +
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Residues in contact with LYS 856 (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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16A GLU 5.9 1.0 + - - -
17A SER* 6.4 0.2 - - - +
20A SER* 4.7 11.3 + - - +
21A ARG* 5.2 0.4 - - - +
24A TYR* 3.9 13.5 - - - +
823A LYS* 3.4 23.8 - - + +
824A ASP* 3.3 27.3 + - - +
826A ASP* 3.7 22.8 + - - -
831A ILE* 3.9 23.9 - - + +
852A ARG 3.0 18.5 + - - +
853A GLN* 3.6 8.3 - - + +
854A LYS 3.3 0.2 - - - -
855A THR* 1.3 78.1 - - - +
857A PHE* 1.3 59.9 + - - +
860A GLY* 3.1 21.8 + - - -
862A ILE* 3.5 16.2 - - + +
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Residues in contact with PHE 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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24A TYR* 3.5 53.1 + + + -
180A GLU* 5.2 9.4 - - - -
853A GLN 3.2 2.2 + - - +
854A LYS* 3.5 13.9 - - + +
856A LYS* 1.3 78.9 - - - +
858A ILE* 1.3 75.1 + - + +
861A ARG* 3.2 8.1 + - - -
862A ILE* 3.1 56.1 + - + +
864A PRO* 3.6 28.5 - - + -
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Residues in contact with ILE 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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609A ILE* 4.6 1.1 - - + -
610A ASP* 3.9 33.9 - - + +
613A ILE* 3.8 37.7 - - + -
614A ALA 5.7 0.2 - - - +
854A LYS* 3.3 36.5 + - - +
855A THR 3.1 3.6 + - - +
857A PHE* 1.3 93.9 - - + +
859A ALA* 1.3 65.7 + - - +
861A ARG* 3.5 15.1 + - - +
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Residues in contact with ALA 859 (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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613A ILE* 3.7 19.3 - - + -
617A LYS* 3.2 42.5 + - + -
821A PHE* 4.2 7.1 - - + -
831A ILE* 5.0 2.7 - - + -
834A ILE* 4.1 22.2 - - + -
855A THR* 2.8 20.1 + - + +
856A LYS 4.8 0.4 - - - +
858A ILE* 1.3 74.8 - - - +
860A GLY* 1.3 60.7 + - - +
861A ARG* 3.3 3.9 + - - +
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Residues in contact with GLY 860 (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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821A PHE* 4.2 12.5 - - - -
823A LYS* 3.6 31.8 - - - +
856A LYS* 3.1 17.6 + - - +
859A ALA* 1.3 77.0 - - - +
861A ARG* 1.3 71.3 + - - +
862A ILE 3.1 4.6 + - - -
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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