Contacts of the helix formed by residues 45 - 56 (chain G) in PDB entry 6CAJ
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 LEU 45 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36G ARG 4.7 10.1 - - - +
44G GLY* 1.3 73.2 - - - -
46G ARG* 1.3 61.9 + - - +
47G ALA 3.4 0.2 - - - -
48G ASN* 3.4 6.6 + - - +
49G LEU* 2.9 29.6 + - - +
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Residues in contact with ARG 46 (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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33G PHE 3.7 13.1 - - - +
34G LEU* 3.3 35.5 - - + +
36G ARG 3.9 14.6 + - - -
44G GLY* 3.5 0.4 - - - -
45G LEU* 1.3 76.0 - - - +
47G ALA* 1.3 59.5 + - - +
49G LEU* 3.4 1.0 + - - -
50G THR* 2.9 29.8 + - - -
93G MET* 6.0 1.1 - - - -
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Residues in contact with ALA 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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44G GLY* 4.2 13.0 + - - +
45G LEU 3.4 0.2 - - - -
46G ARG* 1.3 77.0 - - - +
48G ASN* 1.3 58.0 + - - +
50G THR* 3.4 6.7 + - - -
51G SER* 2.9 30.0 + - - -
93G MET* 4.7 26.6 - - + -
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Residues in contact with ASN 48 (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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44G GLY 3.6 17.2 + - - +
45G LEU* 3.4 7.7 + - - +
46G ARG 3.3 0.4 - - - -
47G ALA* 1.3 79.4 - - - +
49G LEU* 1.3 56.6 + - - +
51G SER* 3.4 5.9 + - - -
52G ALA* 2.9 28.4 + - - +
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Residues in contact with LEU 49 (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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33G PHE* 4.2 19.1 - - + +
36G ARG* 5.7 6.5 - - + -
45G LEU 2.9 17.8 + - - +
46G ARG* 3.8 4.7 - - - +
47G ALA 3.3 0.2 - - - -
48G ASN* 1.3 73.2 - - - +
50G THR* 1.3 60.1 + - - +
52G ALA* 3.3 6.7 + - - +
53G ILE* 2.9 35.8 + - + +
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Residues in contact with THR 50 (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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30G LEU* 3.7 26.2 - - - +
33G PHE* 4.1 4.8 - - - +
34G LEU* 4.9 4.7 - - - -
46G ARG 2.9 17.7 + - - -
47G ALA* 3.7 7.4 - - - -
48G ASN 3.3 0.2 - - - -
49G LEU* 1.3 77.0 - - - +
51G SER* 1.3 56.8 + - - +
53G ILE* 3.3 11.1 - - - +
54G GLU* 2.9 33.9 + - - +
72G PHE* 5.6 4.9 - - - -
93G MET* 6.2 2.7 - - - -
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Residues in contact with SER 51 (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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47G ALA 2.9 17.4 + - - -
48G ASN* 3.7 7.2 - - - -
50G THR* 1.3 75.5 - - - +
52G ALA* 1.3 56.8 + - - +
54G GLU* 3.3 20.2 - - - +
55G THR* 2.9 30.0 + - - -
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Residues in contact with ALA 52 (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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48G ASN 2.9 17.7 + - - +
49G LEU* 3.6 8.3 - - - +
51G SER* 1.3 77.4 - - - +
53G ILE* 1.3 61.5 + - + +
55G THR* 3.4 6.8 + - - -
56G LEU* 2.9 27.5 + - - +
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Residues in contact with ILE 53 (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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6G LEU* 3.7 24.4 - - + +
29G THR* 3.5 41.5 - - + +
30G LEU* 3.7 17.0 - - + -
33G PHE* 3.6 15.5 - - + -
49G LEU* 2.9 17.1 + - + +
50G THR* 3.3 11.2 - - - +
52G ALA* 1.3 80.2 - - + +
54G GLU* 1.3 61.6 + - - +
56G LEU* 3.3 7.6 - - + -
57G CYS* 2.8 31.6 + - - +
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Residues in contact with GLU 54 (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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30G LEU* 3.8 23.5 - - + +
50G THR* 2.9 20.4 + - - +
51G SER* 3.3 24.6 - - - +
53G ILE* 1.3 77.8 - - - +
55G THR* 1.3 61.1 + - - +
57G CYS* 4.0 14.0 + - - +
58G GLY 5.3 0.3 + - - -
69G GLY* 4.4 7.3 - - - +
72G PHE* 5.5 1.2 - - - -
73G LEU* 4.1 25.2 - - - +
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Residues in contact with THR 55 (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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51G SER 2.9 18.9 + - - -
52G ALA* 3.7 6.3 - - - -
54G GLU* 1.3 77.2 - - - +
56G LEU* 1.3 59.6 + - - +
57G CYS 3.5 0.4 - - - -
58G GLY* 4.7 3.6 + - - -
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Residues in contact with LEU 56 (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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6G LEU* 5.8 5.9 - - + +
7G ILE* 5.9 2.4 - - - +
52G ALA 2.9 17.3 + - - +
53G ILE* 3.1 10.7 + - + +
55G THR* 1.3 77.2 - - - +
57G CYS* 1.3 54.4 + - - +
58G GLY 3.3 9.3 + - - -
59G VAL* 6.0 0.3 - - - +
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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