Contacts of the helix formed by residues 19 - 29 (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 ASN 19 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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18C GLY* 1.3 79.1 + - - +
20C ASP* 1.3 67.1 + - - +
21C LEU* 2.8 32.6 + - - +
22C SER* 2.9 18.8 + - - -
25C ARG* 4.5 5.3 + - - +
60C ILE* 3.4 14.0 - - - +
197C LYS 4.0 17.0 - - - +
198C CYS* 4.3 5.4 - - - -
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Residues in contact with ASP 20 (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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19C ASN* 1.3 75.7 - - - +
21C LEU* 1.3 63.5 + - + +
23C ALA* 3.1 21.3 + - - +
24C VAL* 3.5 3.0 + - - -
45C ILE* 3.8 8.9 - - + +
60C ILE* 4.3 1.8 - - - -
197C LYS 4.8 0.2 - - - +
198C CYS* 3.2 17.5 - - - +
199C PRO* 3.3 16.1 - - - +
200C TRP* 3.1 56.1 + - + -
201C THR* 2.9 31.4 + - - +
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Residues in contact with LEU 21 (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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19C ASN* 2.8 19.5 + - - +
20C ASP* 1.3 77.0 - - + +
22C SER* 1.3 57.4 + - - +
23C ALA 3.1 0.4 - - - -
24C VAL* 3.2 8.2 + - + +
25C ARG* 3.0 62.3 + - + +
41C ASP* 3.2 36.6 - - + +
200C TRP* 3.8 25.1 - - + -
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Residues in contact with SER 22 (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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18C GLY* 3.0 25.3 - - - -
19C ASN* 2.9 16.8 + - - -
21C LEU* 1.3 77.2 - - - +
23C ALA* 1.3 59.3 + - - +
25C ARG* 4.1 14.3 + - - +
26C ALA* 3.3 23.2 + - - +
59C HIS* 3.9 26.7 - - - +
60C ILE* 4.1 3.8 - - - -
15D ASP* 4.5 4.7 + - - +
159D PHE* 5.1 2.3 - - - -
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Residues in contact with ALA 23 (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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19C ASN 4.0 0.8 + - - -
20C ASP 3.1 11.1 + - - +
22C SER* 1.3 79.0 - - - +
24C VAL* 1.3 58.3 + - - +
26C ALA 3.5 0.3 + - - -
27C ALA* 2.9 30.7 + - - +
45C ILE* 4.0 4.5 - - + -
48C LEU* 5.1 0.9 - - + -
56C PRO* 3.4 25.5 - - + +
57C PHE* 3.7 35.7 - - + -
60C ILE* 4.1 9.3 - - + +
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Residues in contact with VAL 24 (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 3.5 4.9 + - - +
21C LEU* 3.2 15.2 + - + +
23C ALA* 1.3 75.6 - - - +
25C ARG* 1.3 60.6 + - + +
27C ALA* 3.2 3.6 + - - +
28C ARG* 2.9 69.8 + - - +
41C ASP* 3.6 39.7 - - + +
44C LEU* 4.0 13.0 - - + -
45C ILE* 3.6 19.5 - - + -
200C TRP* 5.6 0.2 - - + -
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Residues in contact with ARG 25 (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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19C ASN* 4.5 6.1 + - - +
21C LEU* 3.0 58.9 + - + +
22C SER* 4.1 12.5 + - - +
24C VAL* 1.3 78.6 - - + +
26C ALA* 1.3 53.8 + - - +
28C ARG* 4.5 3.4 - - - +
29C VAL* 2.8 26.0 + - - -
30C SER* 2.9 34.2 + - - +
31C PHE* 4.8 19.7 - - - +
14D VAL* 5.4 4.7 - - - -
159D PHE* 3.6 14.5 - - + -
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Residues in contact with ALA 26 (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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22C SER 3.3 16.0 + - - +
23C ALA 3.7 4.3 - - - +
24C VAL 3.3 0.2 - - - -
25C ARG* 1.3 76.3 - - - +
27C ALA* 1.3 66.2 + - - +
29C VAL* 3.0 13.5 + - - +
56C PRO* 4.1 5.8 - - + +
59C HIS* 3.4 38.1 - - + +
85D ASN* 3.4 20.4 - - - +
159D PHE* 3.7 17.1 - - + -
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Residues in contact with ALA 27 (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 2.9 19.0 + - - +
24C VAL 3.5 4.9 - - - +
26C ALA* 1.3 77.7 - - - +
28C ARG* 1.3 59.4 + - - +
29C VAL* 4.4 4.2 - - - +
44C LEU* 4.3 11.0 - - + -
48C LEU* 3.8 30.1 - - + -
56C PRO* 3.8 13.0 - - + +
85D ASN* 4.5 4.1 - - - +
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Residues in contact with ARG 28 (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* 2.9 34.0 + - - +
25C ARG* 4.2 2.0 - - - +
27C ALA* 1.3 75.5 - - - +
29C VAL* 1.3 73.1 + - - +
30C SER* 4.0 17.6 - - - -
37C ASP* 6.1 0.2 - - - +
40C ARG* 3.6 38.9 + - - +
41C ASP* 2.8 28.5 + - - -
44C LEU* 3.5 21.9 - - + +
87D LEU* 4.5 5.9 - - - +
157D ARG* 5.6 0.2 + - - -
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Residues in contact with VAL 29 (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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25C ARG 2.8 10.5 + - - -
26C ALA 3.0 15.1 + - - +
27C ALA 4.4 4.7 - - - +
28C ARG* 1.3 82.9 - - - +
30C SER* 1.3 54.2 + - - +
65D HIS* 4.0 1.8 - - - +
85D ASN* 3.5 16.8 - - + +
86D GLU 3.7 20.2 - - - +
87D LEU* 3.7 10.3 - - + +
157D ARG* 2.7 51.8 + - + +
158D PHE* 3.8 26.2 - - - +
159D PHE* 3.8 16.6 - - + +
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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