Contacts of the helix formed by residues 37 - 51 (chain C) in PDB entry 3G4C
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 37 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38C GLU* 1.3 57.3 + - - +
39C GLU* 3.8 6.4 + - - +
40C ARG* 3.1 43.1 + - + +
41C ASP* 2.7 52.7 + - - +
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Residues in contact with GLU 38 (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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37C ASP* 1.3 72.6 + - - +
39C GLU* 1.3 58.3 + - + +
41C ASP* 3.4 2.1 + - - +
42C ARG* 2.8 46.9 + - - +
200C TRP* 3.7 37.1 + - + -
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Residues in contact with GLU 39 (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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37C ASP* 3.4 6.6 + - - +
38C GLU* 1.3 82.1 - - + +
40C ARG* 1.3 57.9 + - - +
42C ARG* 3.9 5.1 - - - +
43C HIS* 2.9 31.2 + - - +
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Residues in contact with ARG 40 (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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28C ARG* 3.6 20.1 + - - +
37C ASP* 3.1 37.0 + - + +
39C GLU* 1.3 74.8 - - - +
41C ASP* 1.3 59.1 + - - +
43C HIS* 3.4 8.0 + - + +
44C LEU* 2.9 28.6 + - - +
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Residues in contact with ASP 41 (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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21C LEU* 3.2 34.6 - - + +
24C VAL* 3.6 9.9 - - + +
28C ARG* 2.8 35.8 + - - +
37C ASP* 2.7 42.9 + - - +
38C GLU* 3.7 4.2 + - - +
40C ARG* 1.3 72.1 - - - +
42C ARG* 1.3 60.4 + - - +
44C LEU* 3.3 4.9 + - - +
45C ILE* 3.1 26.6 + - - +
200C TRP* 3.9 6.7 - - + -
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Residues in contact with ARG 42 (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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38C GLU* 2.8 28.8 + - - +
39C GLU* 3.9 5.6 - - - +
41C ASP* 1.3 70.1 - - - +
43C HIS* 1.3 64.5 + - - +
45C ILE* 3.4 5.9 + - - +
46C GLU* 3.1 35.0 + - + +
200C TRP* 3.1 60.1 - - + +
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Residues in contact with HIS 43 (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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39C GLU 2.9 19.5 + - - +
40C ARG* 3.4 9.3 + - - +
42C ARG* 1.3 73.1 - - - +
44C LEU* 1.3 69.1 + - - +
46C GLU* 3.2 8.1 + - + +
47C TYR* 2.9 39.3 + + + +
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Residues in contact with LEU 44 (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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24C VAL* 4.0 18.6 - - + +
27C ALA* 4.3 8.1 - - + -
28C ARG* 3.5 41.5 - - + +
40C ARG 2.9 13.9 + - - +
41C ASP 3.3 9.6 + - - +
43C HIS* 1.3 81.3 + - - +
45C ILE* 1.3 57.8 + - - +
47C TYR* 3.0 14.9 + - + +
48C LEU* 2.8 53.7 + - + +
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Residues in contact with ILE 45 (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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20C ASP* 3.8 14.6 - - + +
23C ALA* 4.0 5.6 - - + -
24C VAL* 3.6 23.6 - - + +
41C ASP 3.1 14.6 + - - +
42C ARG* 3.6 7.6 - - - +
43C HIS 3.3 0.4 - - - -
44C LEU* 1.3 75.8 - - - +
46C GLU* 1.3 62.5 + - + +
48C LEU* 3.5 6.9 + - + +
49C MET* 3.1 21.7 + - - +
57C PHE* 3.9 27.4 - - + -
200C TRP* 3.8 26.2 - - + +
201C THR* 3.8 33.4 - - - +
204C ALA* 4.0 5.4 - - + -
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Residues in contact with GLU 46 (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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42C ARG* 3.1 22.6 + - + +
43C HIS* 3.2 8.7 + - - +
45C ILE* 1.3 75.1 - - + +
47C TYR* 1.3 58.1 + - - +
50C LYS* 2.9 33.9 + - - +
200C TRP 5.3 1.4 - - - +
203C GLU* 5.0 3.1 - - - +
204C ALA* 4.1 28.3 + - + +
207C LYS* 4.0 28.4 + - - +
208C TYR* 3.8 21.0 + - + +
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Residues in contact with TYR 47 (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 HIS* 2.9 33.9 + + + +
44C LEU* 3.5 17.9 - - + +
46C GLU* 1.3 73.5 - - - +
48C LEU* 1.3 75.9 + - + +
50C LYS* 4.4 3.6 - - + -
51C HIS* 3.0 64.7 + + - +
53C HIS* 4.3 21.9 - + - -
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Residues in contact with LEU 48 (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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23C ALA 4.5 3.4 - - - +
27C ALA* 3.8 26.7 - - + -
44C LEU* 2.8 38.3 + - + +
45C ILE* 3.7 8.1 - - + +
47C TYR* 1.3 85.4 - - + +
49C MET* 1.3 62.6 + - - +
51C HIS 3.3 0.2 + - - -
52C GLY* 3.0 4.7 + - - -
53C HIS* 3.0 60.4 + - + +
56C PRO* 3.8 23.1 - - + -
57C PHE* 3.9 17.0 - - + -
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Residues in contact with MET 49 (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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45C ILE 3.1 12.2 + - - +
46C GLU 3.9 2.9 - - - +
48C LEU* 1.3 78.8 - - - +
50C LYS* 1.3 62.9 + - - +
52C GLY* 3.3 11.8 + - - -
54C GLU* 5.7 8.7 - - - +
57C PHE* 3.9 19.7 - - + -
168C MET* 3.9 16.6 - - - +
201C THR* 3.4 40.6 - - + +
204C ALA* 3.5 29.6 - - + +
205C PHE* 3.4 13.5 - - + +
208C TYR* 3.8 7.8 - - + +
209C ALA* 3.7 28.8 - - + +
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Residues in contact with LYS 50 (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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46C GLU 2.9 19.7 + - - +
47C TYR* 3.9 4.7 - - + +
49C MET* 1.3 79.4 - - - +
51C HIS* 1.3 85.2 + - + +
52C GLY 3.3 1.3 + - - -
208C TYR* 3.6 48.4 + - + +
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Residues in contact with HIS 51 (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 TYR* 3.0 62.7 + + - +
50C LYS* 1.3 105.1 + - + +
52C GLY* 1.3 62.9 + - - +
53C HIS* 3.3 27.9 + - + +
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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
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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