Contacts of the helix formed by residues 40 - 52 (chain B) 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 ARG 40 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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28B ARG* 3.7 13.9 + - - +
41B ASP* 1.3 67.4 + - - +
42B ARG* 3.6 4.2 - - - +
43B HIS* 3.8 16.0 + - - +
44B LEU* 3.2 26.7 + - - +
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Residues in contact with ASP 41 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21B LEU* 3.1 38.3 - - + +
24B VAL* 3.6 14.1 - - + +
28B ARG* 2.9 38.3 + - - +
40B ARG* 1.3 78.3 - - - +
42B ARG* 1.3 64.7 + - - +
44B LEU* 3.2 12.0 + - - +
45B ILE* 3.2 11.4 + - - +
200B TRP* 4.0 9.2 - - + -
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Residues in contact with ARG 42 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40B ARG 4.5 2.3 - - - +
41B ASP* 1.3 77.4 - - - +
43B HIS* 1.3 61.7 + - - +
45B ILE* 3.4 6.0 + - - +
46B GLU* 3.2 37.8 + - + +
199B PRO* 4.4 2.0 + - - +
200B TRP* 3.2 68.1 + - + +
203B GLU* 4.2 28.1 - - - +
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Residues in contact with HIS 43 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40B ARG* 3.8 18.5 + - - +
41B ASP 3.3 0.8 - - - -
42B ARG* 1.3 76.1 - - - +
44B LEU* 1.3 59.9 + - - +
45B ILE 3.4 0.2 - - - -
46B GLU* 3.9 12.4 - - + +
47B TYR* 3.0 27.1 + - + +
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Residues in contact with LEU 44 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24B VAL* 3.7 41.1 - - + +
27B ALA* 4.2 7.2 - - + -
28B ARG* 3.9 23.1 - - + +
40B ARG 3.2 18.2 + - - +
41B ASP 3.2 6.9 + - - +
43B HIS* 1.3 75.9 - - - +
45B ILE* 1.3 60.3 + - - +
47B TYR* 3.4 14.6 - - + +
48B LEU* 2.8 56.6 + - + +
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Residues in contact with ILE 45 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20B ASP* 3.3 43.5 - - + +
23B ALA* 4.8 2.7 - - + -
24B VAL* 3.8 19.1 - - + -
41B ASP 3.2 3.2 + - - +
42B ARG* 3.8 7.9 - - - +
43B HIS 3.4 0.4 - - - -
44B LEU* 1.3 74.7 - - - +
46B GLU* 1.3 60.6 + - + +
48B LEU* 3.3 9.0 + - + +
49B MET* 2.9 29.1 + - - +
57B PHE* 4.2 18.4 - - + -
200B TRP* 3.9 17.7 - - + +
201B THR* 3.8 33.9 - - - +
204B ALA* 3.9 10.5 - - + -
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Residues in contact with GLU 46 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42B ARG* 3.2 34.3 + - + +
43B HIS* 3.9 10.8 - - + +
45B ILE* 1.3 74.3 - - + +
47B TYR* 1.3 53.8 + - - +
49B MET* 3.2 2.1 + - - +
50B LYS* 2.8 41.5 + - - +
200B TRP 5.7 0.4 - - - +
204B ALA* 4.1 18.6 - - + -
207B LYS* 4.2 10.9 + - - -
208B TYR* 2.9 33.6 + - + +
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Residues in contact with TYR 47 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43B HIS* 3.0 19.6 + - + +
44B LEU* 3.4 22.2 - - + +
46B GLU* 1.3 78.3 - - - +
48B LEU* 1.3 71.9 + - + +
50B LYS* 3.4 8.4 + - - +
51B HIS* 2.8 63.4 + + - -
53B HIS* 4.3 21.1 - + - -
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Residues in contact with LEU 48 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23B ALA 4.6 4.3 - - - +
27B ALA* 3.8 31.6 - - + -
44B LEU* 2.8 47.2 + - + +
45B ILE* 3.7 12.3 - - + +
47B TYR* 1.3 81.5 - - + +
49B MET* 1.3 63.6 + - - +
51B HIS 3.3 1.0 + - - -
52B GLY* 3.1 4.5 + - - -
53B HIS* 3.0 61.5 + - + +
56B PRO* 4.3 13.7 - - + -
57B PHE* 4.0 13.2 - - + -
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Residues in contact with MET 49 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45B ILE 2.9 17.0 + - - +
46B GLU 3.6 3.1 - - - +
48B LEU* 1.3 77.5 - - - +
50B LYS* 1.3 62.6 + - - +
51B HIS 3.4 0.5 + - - -
52B GLY* 3.4 8.9 + - - -
53B HIS 6.0 0.2 - - - -
54B GLU* 6.4 2.7 - - - -
57B PHE* 3.8 23.5 - - + -
168B MET* 3.8 17.7 - - - +
201B THR* 3.3 43.3 - - + +
204B ALA* 3.3 33.9 - - + +
205B PHE* 3.6 6.7 - - - +
208B TYR* 3.9 8.8 - - + +
209B ALA* 3.8 30.4 - - + +
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Residues in contact with LYS 50 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46B GLU* 2.8 22.5 + - - +
47B TYR* 3.7 9.0 - - - +
49B MET* 1.3 74.7 - - - +
51B HIS* 1.3 85.0 + - + +
52B GLY 3.7 0.2 + - - -
208B TYR* 3.7 50.3 + - + +
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Residues in contact with HIS 51 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47B TYR* 2.8 62.7 + + - +
50B LYS* 1.3 105.2 - - + +
52B GLY* 1.3 61.9 + - - +
53B HIS* 3.4 27.4 + + + +
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Residues in contact with GLY 52 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48B LEU 3.1 4.7 + - - -
49B MET* 3.4 7.5 + - - -
50B LYS 3.4 3.0 + - - -
51B HIS* 1.3 79.6 - - - +
53B HIS* 1.3 61.4 + - - +
54B GLU* 3.1 24.7 + - - +
173D LEU* 5.4 8.0 - - - +
211D LYS* 6.1 3.1 - - - -
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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