Contacts of the helix formed by residues 51 - 63 (chain C) in PDB entry 4G8O
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 GLY 51 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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50C THR* 1.3 74.8 - - - +
52C GLY* 1.3 66.4 + - - -
53C GLU 3.6 0.5 + - - -
54C THR 3.6 0.9 + - - -
55C GLN* 3.6 16.1 + - - -
305C ASP* 3.0 39.8 + - - +
306C PHE* 4.7 0.2 - - - +
307C THR* 4.0 10.0 + - - -
308C SER* 4.0 4.5 - - - -
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Residues in contact with GLY 52 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51C GLY* 1.3 70.9 - - - -
53C GLU* 1.4 62.0 + - - -
55C GLN* 3.7 8.5 + - - +
56C GLN* 3.3 19.8 + - - +
305C ASP* 3.9 6.0 + - - -
307C THR* 5.1 0.2 + - - -
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Residues in contact with GLU 53 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51C GLY 3.6 0.4 + - - -
52C GLY* 1.4 69.7 - - - -
54C THR* 1.4 60.2 + - - +
56C GLN* 3.3 10.2 + - - +
57C GLN* 3.1 33.1 + - + +
297C ASP* 3.9 13.5 - - - +
303C GLN 6.1 0.2 - - - +
305C ASP* 5.3 2.4 - - + +
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Residues in contact with THR 54 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50C THR* 3.9 18.2 - - + -
51C GLY 3.6 8.9 + - - -
52C GLY 3.4 0.2 - - - -
53C GLU* 1.4 76.5 - - - +
55C GLN* 1.3 60.2 + - - +
57C GLN* 3.5 12.5 + - - +
58C ILE* 3.6 17.6 + - + +
297C ASP* 3.5 20.3 + - - +
298C MET* 3.8 37.7 - - + +
303C GLN 3.7 3.6 + - - -
305C ASP* 3.1 32.3 + - - +
306C PHE* 4.7 2.0 - - + -
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Residues in contact with GLN 55 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47C GLN* 3.9 10.8 + - + +
48C LEU* 5.8 0.4 - - - +
50C THR* 3.2 38.9 + - - +
51C GLY* 3.6 17.2 + - - +
52C GLY 3.7 12.8 + - - +
53C GLU 3.3 0.4 - - - -
54C THR* 1.3 76.1 - - - +
56C GLN* 1.4 58.2 + - - +
58C ILE* 3.3 5.1 + - - +
59C GLN* 3.1 62.6 + - + +
67C ASP* 5.0 9.1 + - - -
308C SER* 4.9 2.4 + - - -
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Residues in contact with GLN 56 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52C GLY 3.3 11.6 + - - +
53C GLU* 3.3 14.0 + - - +
55C GLN* 1.4 78.4 + - - +
57C GLN* 1.4 56.2 + - + +
59C GLN* 4.1 10.3 - - - +
60C ALA* 3.2 30.1 + - - +
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Residues in contact with GLN 57 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53C GLU* 3.1 15.6 + - + +
54C THR* 3.6 9.0 - - - +
55C GLN 3.3 0.2 - - - -
56C GLN* 1.4 76.1 - - - +
58C ILE* 1.4 59.9 + - - +
60C ALA* 3.8 4.6 + - - +
61C ALA* 3.5 17.7 + - - +
293C LEU 5.4 0.2 - - - +
294C GLY* 3.2 28.0 + - - +
295C MET* 3.5 17.3 - - + +
296C THR* 3.2 24.7 + - - -
297C ASP* 2.8 40.1 + - - +
298C MET 4.7 0.7 + - - -
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Residues in contact with ILE 58 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43C LEU* 3.9 18.6 - - + +
46C LEU* 3.9 21.3 - - + +
47C GLN* 3.8 20.0 - - + -
50C THR* 3.8 31.4 - - + +
54C THR* 3.6 17.7 - - + +
55C GLN 3.3 5.0 + - - +
57C GLN* 1.4 74.0 - - + +
59C GLN* 1.3 58.1 + - - +
61C ALA* 3.3 2.9 + - - +
62C MET* 2.9 48.1 + - + +
295C MET* 3.8 23.8 - - + -
298C MET* 4.4 9.2 - - + -
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Residues in contact with GLN 59 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128B GLU* 4.4 3.4 - - - +
47C GLN* 3.5 27.6 + - + +
55C GLN* 3.1 53.8 + - - +
56C GLN* 4.2 7.6 - - - +
58C ILE* 1.3 75.2 - - - +
60C ALA* 1.4 56.3 + - - +
62C MET 4.7 0.2 - - - +
63C GLY* 3.0 22.9 + - - -
64C PHE 3.4 19.8 + - - +
65C LYS* 3.5 47.1 + - + +
66C ILE* 4.9 1.6 - - - +
67C ASP* 5.5 4.6 + - - +
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Residues in contact with ALA 60 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127B SER* 3.6 26.1 - - - +
128B GLU* 3.4 38.7 - - - +
129B VAL* 4.1 4.2 + - - +
130B GLU 5.3 0.5 + - - -
56C GLN 3.2 19.4 + - - +
57C GLN* 4.0 5.6 - - - +
58C ILE 3.2 0.2 - - - -
59C GLN* 1.4 77.3 - - - +
61C ALA* 1.3 62.4 + - - +
63C GLY* 3.6 9.5 + - - -
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Residues in contact with ALA 61 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127B SER 4.9 2.9 - - - -
129B VAL* 5.3 6.6 - - - +
15C PHE* 3.3 11.9 - - + -
18C ARG* 2.9 30.0 + - - +
57C GLN 3.5 14.6 + - - +
58C ILE 3.3 3.2 + - - +
60C ALA* 1.3 76.8 - - - +
62C MET* 1.3 58.5 + - - +
293C LEU* 4.0 19.7 - - + +
295C MET* 3.7 27.1 - - + -
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Residues in contact with MET 62 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130B GLU* 5.0 1.0 - - - +
11C LEU* 3.8 18.7 - - - +
15C PHE* 3.7 41.1 - - + +
18C ARG* 4.3 4.3 + - - -
40C ALA* 3.3 30.1 - - + +
43C LEU* 3.8 20.9 - - - -
44C ALA* 4.1 2.5 - - + +
47C GLN* 3.2 26.2 - - - +
58C ILE* 2.9 24.3 + - + +
59C GLN 4.4 1.6 - - - +
61C ALA* 1.3 76.7 - - - +
63C GLY* 1.3 60.2 + - - +
64C PHE* 3.5 42.1 - - + +
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Residues in contact with GLY 63 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128B GLU* 5.3 5.6 - - - -
130B GLU* 4.5 12.5 - - - +
131B ARG* 5.9 1.1 - - - -
7C TYR* 5.1 2.8 + - - -
11C LEU* 3.6 18.1 - - - +
59C GLN 3.0 11.6 + - - -
60C ALA 3.6 8.0 + - - -
61C ALA 3.5 2.0 - - - -
62C MET* 1.3 77.8 - - - +
64C PHE* 1.3 61.8 + - - +
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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