Contacts of the helix formed by residues 44 - 52 (chain G) in PDB entry 6C3P
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 PHE 44 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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77C MET* 3.4 30.5 - - + -
81C CYS* 6.2 0.9 - - + -
40G LEU* 3.0 51.0 + - + +
41G PHE* 4.9 6.7 - + + +
43G THR* 1.3 75.9 - - - +
45G PRO* 1.3 59.6 - - + +
47G LEU* 2.8 9.8 + - + -
48G PHE* 2.7 59.3 + + + -
119G THR* 3.6 34.8 - - + -
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Residues in contact with PRO 45 (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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74C ILE* 4.8 17.9 - - + +
77C MET* 5.1 4.7 - - + +
78C SER* 4.5 17.5 - - - +
81C CYS* 4.2 19.7 - - - -
41G PHE 3.7 13.5 - - - +
42G ILE 4.0 5.4 - - - +
43G THR 3.7 3.1 - - - -
44G PHE* 1.3 93.1 - - + +
46G ILE* 1.3 60.8 + - + +
47G LEU 3.0 0.2 + - - -
48G PHE* 3.1 8.5 + - + +
49G ILE* 2.9 35.6 + - + +
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Residues in contact with ILE 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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59C VAL* 5.6 10.3 - - + -
42G ILE* 3.8 16.8 - - + +
43G THR* 3.2 22.0 - - + +
45G PRO* 1.3 78.1 - - + +
47G LEU* 1.3 58.1 + - - +
49G ILE* 3.3 28.2 - - + +
123G TYR* 3.3 37.7 - - + +
127G ILE* 5.3 5.7 - - - +
135G LEU* 6.3 0.9 - - + -
138G ALA* 6.4 1.3 - - + -
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Residues in contact with LEU 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 THR* 2.9 15.3 + - - +
44G PHE* 2.8 13.9 + - + +
46G ILE* 1.3 80.6 - - - +
48G PHE* 1.3 69.3 + - + +
49G ILE 3.1 1.3 - - - -
50G GLY* 3.3 3.2 + - - -
51G TRP* 2.9 44.9 + - + +
119G THR* 6.0 4.0 - - + -
122G VAL* 4.6 12.6 - - + -
123G TYR* 4.5 23.1 - - + +
126G ASN* 3.4 37.7 - - + +
127G ILE* 6.5 0.4 - - + -
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Residues in contact with PHE 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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73C LEU* 4.6 15.7 - - + -
74C ILE* 3.8 24.7 - - + +
77C MET* 3.5 37.0 - - + -
44G PHE* 2.7 56.0 + + + +
45G PRO* 3.7 6.5 - - + +
47G LEU* 1.3 76.6 - - + +
49G ILE* 1.3 63.9 + - - +
50G GLY 3.2 0.4 - - - -
51G TRP* 4.2 24.5 - + + +
52G GLY* 3.1 24.3 + - - +
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Residues in contact with ILE 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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59C VAL* 5.8 18.8 - - + +
62C THR* 5.6 11.1 - - - +
63C LEU* 5.0 9.6 - - + -
66C LEU* 4.6 14.2 - - + +
74C ILE* 4.2 23.1 - - + -
45G PRO 2.9 18.7 + - - +
46G ILE* 3.3 33.2 - - + +
47G LEU* 5.3 0.2 - - - -
48G PHE* 1.3 78.4 - - - +
50G GLY* 1.3 75.0 + - - +
52G GLY* 4.8 2.6 + - - -
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Residues in contact with GLY 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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47G LEU 3.3 3.3 + - - -
48G PHE 3.2 0.2 - - - -
49G ILE* 1.3 93.0 - - - +
51G TRP* 1.3 63.4 + - - +
52G GLY 3.4 3.4 + - - -
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Residues in contact with TRP 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 LEU* 2.9 35.0 + - + +
48G PHE* 4.2 20.6 - + - -
50G GLY* 1.3 80.4 - - - +
52G GLY* 1.3 66.8 + - - +
122G VAL* 5.8 5.2 - - + -
126G ASN* 4.7 18.6 - - - +
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Residues in contact with GLY 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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66C LEU* 6.3 1.8 - - - -
70C HIS* 3.4 43.3 + - - -
74C ILE* 6.1 0.2 - - - -
48G PHE* 3.1 25.5 + - - +
49G ILE 5.5 2.0 - - - -
50G GLY 3.4 4.6 - - - -
51G TRP* 1.3 87.2 - - - +
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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