Contacts of the helix formed by residues 29 - 47 (chain G) in PDB entry 6CMO
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 LYS 29 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24B ALA 3.4 16.1 + - - +
25B CYS* 4.9 11.4 - - - +
27B ASP* 3.1 30.7 + - - -
27G ARG 3.7 4.0 + - - +
28G ILE* 1.3 77.6 - - - +
30G VAL* 1.3 68.0 + - - +
31G SER* 3.2 13.2 + - - +
32G LYS* 3.4 30.8 - - - +
33G ALA* 3.3 19.9 + - - +
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Residues in contact with VAL 30 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B CYS* 3.3 38.5 - - + +
27B ASP* 4.5 2.9 - - - +
28B ALA* 3.7 26.9 - - + +
30B LEU* 5.1 11.8 - - + +
257B ALA* 4.0 23.6 - - + -
259B GLN* 5.1 4.5 - - + +
261B LEU* 4.8 17.6 - - + +
28G ILE 4.7 0.4 - - - +
29G LYS* 1.3 73.7 - - + +
31G SER* 1.3 62.0 + - - +
33G ALA* 3.9 7.7 - - - +
34G ALA* 2.9 30.7 + - - +
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Residues in contact with SER 31 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28B ALA* 5.4 8.1 - - - -
33B ILE* 5.3 9.7 - - - +
29G LYS* 4.1 14.2 - - - +
30G VAL* 1.3 82.4 - - - +
32G LYS* 1.3 70.4 + - - +
34G ALA* 3.2 7.3 + - - +
35G ALA* 2.9 25.6 + - - +
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Residues in contact with LYS 32 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28G ILE* 3.8 20.2 - - + -
29G LYS* 3.4 39.1 - - - +
31G SER* 1.3 82.4 + - - +
33G ALA* 1.3 63.6 + - - +
35G ALA* 3.3 10.8 + - + +
36G ASP* 2.9 25.6 + - - +
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Residues in contact with ALA 33 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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254B ASP* 4.0 20.6 - - - +
256B ARG* 4.6 15.0 - - + +
257B ALA* 5.4 2.2 - - + -
261B LEU* 6.5 1.1 - - + -
28G ILE* 4.7 4.0 - - + -
29G LYS 3.3 17.9 + - - +
30G VAL* 3.9 8.3 - - - +
32G LYS* 1.3 76.4 - - - +
34G ALA* 1.3 59.5 + - - +
36G ASP* 3.1 10.1 + - - +
37G LEU* 3.0 33.3 + - + +
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Residues in contact with ALA 34 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30B LEU* 5.8 8.1 - - + -
33B ILE* 3.9 30.8 - - + +
261B LEU* 6.5 1.1 - - + -
30G VAL 2.9 20.9 + - - +
31G SER* 3.4 5.8 - - - +
33G ALA* 1.3 75.7 - - - +
35G ALA* 1.3 57.0 + - - +
37G LEU* 3.3 12.9 + - + +
38G MET* 2.9 31.2 + - - +
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Residues in contact with ALA 35 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B ILE* 5.9 0.8 - - - +
31G SER 2.9 14.2 + - - +
32G LYS* 3.4 14.8 - - + +
33G ALA 3.2 0.4 - - - -
34G ALA* 1.3 73.9 - - - +
36G ASP* 1.3 60.3 + - - +
38G MET* 3.4 14.6 - - + +
39G ALA* 2.9 31.6 + - - +
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Residues in contact with ASP 36 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237B ASN* 4.4 12.9 + - - -
239B ASN* 4.4 19.1 - - - +
256B ARG* 5.5 5.0 + - - -
32G LYS 2.9 13.7 + - - +
33G ALA* 3.1 13.0 + - - +
35G ALA* 1.3 76.0 - - - +
37G LEU* 1.3 57.9 + - + +
39G ALA* 3.7 4.7 - - - +
40G TYR* 3.0 31.2 + - - +
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Residues in contact with LEU 37 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235B PHE* 4.4 20.9 - - + -
237B ASN* 5.7 2.5 - - - +
239B ASN* 5.5 6.1 - - + +
240B ALA* 4.2 22.9 - - + -
252B LEU* 5.2 15.3 - - + -
254B ASP* 6.0 2.9 - - - +
261B LEU* 5.3 11.2 - - + -
300B LEU* 5.2 13.2 - - + -
33G ALA* 3.0 21.7 + - + +
34G ALA* 3.3 13.0 + - + +
36G ASP* 1.3 78.7 - - + +
38G MET* 1.3 57.5 + - - +
40G TYR* 3.6 3.2 + - - +
41G CYS* 2.9 38.1 + - - +
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Residues in contact with MET 38 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B ILE* 4.9 14.8 - - + +
36B ASN* 6.0 4.3 - - + +
37B ILE* 4.8 20.9 - - + -
300B LEU* 4.8 15.4 - - + +
34G ALA 2.9 21.4 + - - +
35G ALA* 3.4 16.6 - - - +
37G LEU* 1.3 77.8 - - - +
39G ALA* 1.3 65.8 + - - +
41G CYS* 3.8 5.7 - - - +
42G GLU* 2.9 37.6 + - + +
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Residues in contact with ALA 39 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35G ALA 2.9 20.7 + - - +
36G ASP* 3.7 6.5 - - - +
38G MET* 1.3 80.6 - - - +
40G TYR* 1.3 62.4 + - - +
42G GLU* 3.3 15.9 - - - +
43G ALA* 3.0 28.8 + - - +
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Residues in contact with TYR 40 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235B PHE* 3.4 36.3 - + + -
236B PRO* 3.5 22.9 - - + +
237B ASN* 4.5 21.5 - - + +
280B LYS 3.5 18.3 + - - -
281B SER 3.8 14.8 - - - -
36G ASP* 3.0 18.7 + - - +
37G LEU 4.2 1.8 - - - +
39G ALA* 1.3 75.9 - - - +
41G CYS* 1.3 57.0 + - - +
43G ALA* 3.7 6.6 - - + +
44G HIS* 2.9 44.2 + + + +
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Residues in contact with CYS 41 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235B PHE* 4.0 14.1 - - - -
281B SER 4.0 18.9 - - - +
282B GLY 4.0 19.1 - - - -
283B ARG* 4.2 11.0 + - + +
299B ALA* 6.1 0.2 - - - -
300B LEU* 4.3 23.3 - - + -
37G LEU* 2.9 27.8 + - - +
38G MET* 4.0 6.7 - - - +
40G TYR* 1.3 78.2 - - - +
42G GLU* 1.3 50.0 + - - +
45G ALA* 2.5 39.8 + - - +
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Residues in contact with GLU 42 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38G MET* 2.9 30.9 + - + +
39G ALA* 3.3 19.0 - - - +
41G CYS* 1.3 75.5 - - - +
43G ALA* 1.3 75.8 + - - +
45G ALA* 3.8 4.1 - - - +
46G LYS* 2.9 30.0 + - - +
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Residues in contact with ALA 43 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39G ALA 3.0 19.0 + - - +
40G TYR* 3.7 9.4 - - + +
42G GLU* 1.3 85.7 - - - +
44G HIS* 1.3 59.5 + - + +
46G LYS* 3.1 10.0 + - - +
47G GLU* 3.0 26.3 + - - +
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Residues in contact with HIS 44 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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280B LYS* 3.3 63.4 - - + +
281B SER* 3.3 14.6 - - - -
40G TYR* 2.9 34.0 + - + +
43G ALA* 1.3 72.2 - - + +
45G ALA* 1.3 59.6 + - - +
47G GLU* 3.2 31.5 + - + +
48G ASP* 2.9 22.8 + - - -
49G PRO* 4.6 2.0 - - - +
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Residues in contact with ALA 45 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281B SER* 4.1 6.9 - - - -
283B ARG* 4.9 17.7 - - + +
41G CYS 2.5 26.8 + - - +
42G GLU* 3.8 5.6 - - - +
44G HIS* 1.3 76.0 - - - +
46G LYS* 1.3 62.1 + - - +
47G GLU 3.2 0.2 - - - -
48G ASP* 3.3 20.1 + - - +
51G LEU* 4.3 25.1 - - + +
52G THR* 4.8 2.4 + - - -
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Residues in contact with LYS 46 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42G GLU* 2.9 15.5 + - - +
43G ALA* 3.1 9.8 + - - +
45G ALA* 1.3 76.9 - - - +
47G GLU* 1.3 75.9 + - + +
48G ASP 3.3 1.7 + - - +
52G THR* 4.5 8.4 + - - -
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Residues in contact with GLU 47 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43G ALA 3.0 15.3 + - - +
44G HIS* 3.2 38.2 + - + +
45G ALA 3.2 0.4 - - - -
46G LYS* 1.3 98.2 + - + +
48G ASP* 1.3 57.1 + - - +
49G PRO* 3.3 13.9 - - - +
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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
------------------------------------------------------------
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