Contacts of the helix formed by residues 15 - 24 (chain B) in PDB entry 3JCA
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 15 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13B HIS 3.9 0.6 + - - -
14B GLN* 1.3 77.2 - - - +
16B ALA* 1.3 63.8 + - - +
17B ALA* 3.8 7.0 - - - +
18B ALA* 2.9 33.3 + - - +
19B LEU* 3.0 19.3 + - - +
34B VAL* 4.4 4.3 - - - -
170B LYS* 5.4 2.4 - - - +
195B ASN* 2.9 22.4 + - - +
196B MET 2.8 31.0 + - - +
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Residues in contact with ALA 16 (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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15B ASN* 1.3 71.0 - - - +
17B ALA* 1.3 60.6 + - - +
19B LEU* 4.1 7.2 - - - -
20B ARG* 2.9 35.2 + - - +
27B ARG* 4.9 5.6 - - + +
30B ALA* 3.5 33.4 - - + +
31B ARG* 4.1 11.7 - - + +
34B VAL* 3.9 10.1 - - + +
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Residues in contact with ALA 17 (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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15B ASN* 3.2 5.6 + - - +
16B ALA* 1.3 80.0 - - - +
18B ALA* 1.3 63.3 + - - +
20B ARG* 3.4 8.6 - - - +
21B PHE* 2.9 40.8 + - + -
196B MET 3.4 24.2 - - - +
197B ASP 3.8 15.9 - - - +
198B ASN* 5.1 6.1 - - - +
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Residues in contact with ALA 18 (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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14B GLN* 3.8 17.9 - - + -
15B ASN* 2.9 23.0 + - - +
17B ALA* 1.3 75.7 - - - +
19B LEU* 1.3 63.7 + - - +
21B PHE* 4.1 0.7 - - - +
22B GLN* 3.2 26.2 + - - +
194B VAL* 3.3 26.2 - - + +
196B MET* 3.7 20.3 - - + +
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Residues in contact with LEU 19 (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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5B ALA* 3.5 30.7 - - + +
9B HIS* 3.9 7.2 - - + +
14B GLN* 3.4 41.1 - - + +
15B ASN 3.0 18.1 + - - +
16B ALA* 3.6 7.0 - - - +
18B ALA* 1.3 78.5 - - - +
20B ARG* 1.3 57.5 + - - +
23B PHE* 3.0 30.3 + - + -
25B ILE* 3.4 18.8 - - + +
30B ALA* 3.9 17.0 - - + +
33B ILE* 3.8 25.6 - - + -
34B VAL* 4.0 6.3 - - + -
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Residues in contact with ARG 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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16B ALA 2.9 21.7 + - - +
17B ALA* 3.4 11.4 - - - +
19B LEU* 1.3 76.2 - - - +
21B PHE* 1.3 93.5 + - + +
24B HIS* 2.7 29.2 + - - -
25B ILE* 3.0 39.4 + - + +
26B THR* 4.7 1.2 - - - +
27B ARG* 3.4 43.0 - - - +
30B ALA* 4.0 3.6 - - + -
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Residues in contact with PHE 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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17B ALA* 2.9 33.2 + - + +
20B ARG* 1.3 110.9 - - + +
22B GLN* 1.3 63.1 + - - +
24B HIS* 3.8 16.3 + - - -
196B MET* 3.7 17.9 - - + -
197B ASP 3.4 22.2 - - - -
198B ASN* 3.7 18.6 - - - -
199B GLN 4.8 1.3 - - - -
200B GLY* 3.5 24.5 - - - -
248B GLN* 5.6 1.4 - - - +
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Residues in contact with GLN 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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18B ALA 3.2 17.6 + - - +
21B PHE* 1.3 80.3 - - - +
23B PHE* 1.3 89.3 + - + +
24B HIS* 3.6 11.5 + - - -
196B MET* 5.0 12.0 - - + +
248B GLN* 2.8 24.1 + - - +
249B ASP* 2.8 29.7 + - - -
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Residues in contact with PHE 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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1B ALA* 3.6 27.5 - - + +
2B LEU* 4.2 11.9 - - + +
4B SER* 3.1 29.2 - - - -
5B ALA* 3.5 28.3 - - + -
8B SER* 4.4 10.5 - - - -
14B GLN* 5.2 4.7 - - - -
19B LEU* 3.0 22.7 + - - +
22B GLN* 1.3 100.7 - - + +
24B HIS* 1.3 77.6 + - - +
25B ILE* 3.3 15.1 + - + +
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Residues in contact with HIS 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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2B LEU* 5.3 1.4 - - - +
20B ARG* 2.7 21.3 + - - -
21B PHE* 3.8 17.2 + - - -
22B GLN 3.6 10.0 + - - -
23B PHE* 1.3 79.7 - - - +
25B ILE* 1.3 58.7 + - - +
26B THR 4.1 0.9 + - - -
231B GLY 6.1 1.3 - - - -
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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