Contacts of the helix formed by residues 19 - 29 (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 ASN 19 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18B GLY* 1.3 78.3 - - - +
20B ASP* 1.3 65.4 + - + +
21B LEU* 2.8 31.5 + - - +
22B SER* 2.9 21.1 + - - -
60B ILE* 3.4 14.4 - - - +
197B LYS 4.0 12.3 - - - +
198B CYS* 4.2 11.4 - - - -
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Residues in contact with ASP 20 (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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19B ASN* 1.3 77.9 - - - +
21B LEU* 1.3 61.3 + - + +
23B ALA* 3.4 12.6 + - - +
24B VAL 3.4 4.2 + - - -
45B ILE* 3.3 21.9 - - + +
60B ILE* 4.4 2.5 - - - -
197B LYS 4.6 0.3 - - - +
198B CYS* 3.3 15.7 - - - +
199B PRO* 3.2 27.4 - - - +
200B TRP* 3.2 41.9 + - + +
201B THR* 2.8 34.2 + - - -
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Residues in contact with LEU 21 (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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19B ASN* 2.8 21.1 + - - +
20B ASP* 1.3 70.8 - - + +
22B SER* 1.3 59.6 + - - +
23B ALA 3.2 0.2 - - - -
24B VAL* 3.5 9.9 - - + +
25B ARG* 2.9 31.5 + - - +
41B ASP* 3.1 31.9 - - + +
200B TRP* 3.7 30.1 - - + -
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Residues in contact with SER 22 (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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15A ASP* 4.6 3.5 + - - -
159A PHE* 5.1 0.5 - - - -
18B GLY* 3.1 27.8 - - - -
19B ASN* 2.9 14.1 + - - -
21B LEU* 1.3 78.8 - - - +
23B ALA* 1.3 59.2 + - - +
25B ARG* 3.4 11.5 - - - +
26B ALA* 3.3 24.3 + - - +
59B HIS* 3.9 26.3 - - - +
60B ILE* 4.0 4.7 - - - -
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Residues in contact with ALA 23 (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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19B ASN 3.9 0.8 + - - -
20B ASP 3.4 10.4 + - - +
21B LEU 3.2 0.4 - - - -
22B SER* 1.3 75.5 - - - +
24B VAL* 1.3 61.0 + - - +
26B ALA* 3.8 0.2 - - - +
27B ALA* 2.9 32.0 + - - +
45B ILE* 4.8 2.2 - - + -
48B LEU* 5.0 2.2 - - + -
56B PRO* 3.4 29.1 - - + +
57B PHE* 3.7 33.4 - - + -
60B ILE* 4.1 8.9 - - + +
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Residues in contact with VAL 24 (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 3.4 12.5 + - - +
21B LEU* 3.2 22.5 + - + +
23B ALA* 1.3 77.3 - - - +
25B ARG* 1.3 59.3 + - - +
27B ALA* 3.3 3.3 + - - +
28B ARG* 3.0 64.9 + - - +
41B ASP* 3.6 31.9 - - + +
44B LEU* 3.7 14.8 - - + +
45B ILE* 3.8 14.1 - - + -
48B LEU* 5.3 0.4 - - - -
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Residues in contact with ARG 25 (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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14A VAL* 5.0 8.1 - - + -
159A PHE* 3.6 19.3 - - + -
21B LEU 2.9 15.8 + - - +
22B SER* 3.4 17.5 - - - +
24B VAL* 1.3 74.3 - - + +
26B ALA* 1.3 58.6 + - - +
28B ARG* 3.3 3.7 + - - +
29B VAL* 2.6 32.2 + - - -
30B SER* 3.0 32.5 + - - +
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Residues in contact with ALA 26 (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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85A ASN* 3.3 22.7 - - - +
159A PHE* 3.8 19.3 - - + -
22B SER 3.3 13.4 + - - +
23B ALA 3.8 3.8 - - - +
25B ARG* 1.3 81.8 - - - +
27B ALA* 1.3 60.3 + - - +
29B VAL* 3.3 12.1 + - - +
56B PRO* 4.2 1.6 - - + +
59B HIS* 3.2 41.3 - - + +
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Residues in contact with ALA 27 (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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85A ASN* 4.9 2.9 - - - -
23B ALA 2.9 18.8 + - - +
24B VAL 3.5 4.7 - - - +
26B ALA* 1.3 76.9 - - - +
28B ARG* 1.3 61.1 + - - +
29B VAL* 3.6 3.5 + - - +
44B LEU* 4.2 8.7 - - + -
48B LEU* 3.8 31.4 - - + -
56B PRO* 4.0 13.4 - - + +
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Residues in contact with ARG 28 (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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157A ARG* 5.4 1.6 + - - -
24B VAL* 3.0 35.9 + - - +
25B ARG* 3.9 3.8 - - - +
27B ALA* 1.3 75.7 - - - +
29B VAL* 1.3 70.6 - - - +
30B SER* 4.0 20.3 + - - +
40B ARG* 3.7 25.1 + - - +
41B ASP* 2.9 33.5 + - - +
44B LEU* 3.9 17.6 - - + +
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Residues in contact with VAL 29 (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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65A HIS* 4.1 1.3 - - - +
85A ASN* 3.8 17.3 - - + +
86A GLU 4.0 18.2 - - - +
87A LEU* 4.0 7.0 - - + +
157A ARG* 2.7 71.1 + - + +
158A PHE* 4.0 2.0 - - - +
159A PHE* 4.0 21.3 - - + -
25B ARG 2.6 14.3 + - - -
26B ALA 3.3 14.8 - - - +
27B ALA 3.3 4.2 - - - +
28B ARG* 1.3 76.6 - - - +
30B SER* 1.3 54.5 + - - +
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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