Contacts of the helix formed by residues 20 - 36 (chain B) in PDB entry 3C3K
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 20 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16B SER* 5.1 2.8 + - - -
17B ASN* 2.9 24.4 + - + +
18B ILE 4.3 2.8 - - - +
19B ALA* 1.3 76.5 - - - +
21B PRO* 1.3 76.1 - - - +
22B PHE* 3.2 17.5 + - - +
23B CYS* 2.9 28.0 + - - +
24B ALA* 3.4 6.9 + - - +
138B TYR* 5.3 1.0 + - - -
166B LEU* 3.4 28.6 - - + +
192B SER* 4.7 2.9 + - - -
220B ASP* 4.5 1.6 - - - +
303B GOL 3.1 32.6 + - - -
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Residues in contact with PRO 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 ALA 3.3 10.3 - - - +
20B ASN* 1.3 88.3 - - - +
22B PHE* 1.3 60.4 + - - +
24B ALA* 3.4 11.7 + - + +
25B ALA* 3.2 21.8 + - - +
194B VAL* 3.7 29.4 - - + -
222B VAL* 3.8 26.2 - - + +
301B CL 3.7 22.9 - - + -
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Residues in contact with PHE 22 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B SER* 5.8 0.4 - - - -
20B ASN* 3.0 12.5 + - - +
21B PRO* 1.3 75.5 - - - +
23B CYS* 1.3 70.8 + - - +
25B ALA* 3.2 5.5 + - - +
26B VAL* 2.9 43.8 + - + +
71B MET* 3.7 16.6 - - + -
93B ALA* 4.0 13.7 - - + -
220B ASP* 3.4 33.0 - - + +
222B VAL* 3.9 9.5 - - + +
237B GLN* 3.5 26.0 - - + -
239B SER* 3.3 28.0 - - - -
242B ILE* 4.5 7.0 - - + -
303B GOL 3.7 34.3 - - - +
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Residues in contact with CYS 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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15B VAL* 3.7 17.7 - - + -
16B SER* 3.3 25.8 - - - -
17B ASN 3.2 28.0 - - - +
18B ILE* 4.8 2.5 - - + +
20B ASN* 2.9 21.4 + - - +
22B PHE* 1.3 79.8 - - - +
24B ALA* 1.3 57.0 + - - +
26B VAL* 3.1 2.6 + - - +
27B VAL* 2.8 33.8 + - + +
71B MET* 4.0 19.1 - - - -
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Residues in contact with ALA 24 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A ILE* 4.5 16.1 - - + +
19A ALA* 4.1 35.4 - - + +
18B ILE 5.3 4.2 + - - +
20B ASN 3.4 3.5 + - - +
21B PRO* 3.4 16.7 + - + +
22B PHE 3.3 0.8 - - - -
23B CYS* 1.3 78.4 - - - +
25B ALA* 1.3 57.3 + - - +
27B VAL* 3.8 6.4 - - - +
28B LYS* 3.0 27.5 + - - +
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Residues in contact with ALA 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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21B PRO 3.2 13.4 + - - +
22B PHE* 3.6 6.5 - - - +
23B CYS 3.2 0.2 - - - -
24B ALA* 1.3 74.7 - - - +
26B VAL* 1.3 65.7 + - - +
28B LYS* 3.4 14.7 + - - +
29B GLY 3.4 8.7 + - - -
222B VAL* 5.4 4.7 - - + -
239B SER* 3.5 25.4 - - - +
240B GLU* 3.7 13.9 - - + +
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Residues in contact with VAL 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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22B PHE* 2.9 51.8 + - + +
23B CYS 3.7 5.4 - - - +
25B ALA* 1.3 76.4 - - - +
27B VAL* 1.3 64.8 + - - +
29B GLY 3.0 3.3 + - - -
30B ILE* 2.9 32.4 + - + +
71B MET* 3.8 16.8 - - + -
92B CYS* 4.3 12.6 - - - -
239B SER* 3.6 17.9 - - - +
242B ILE* 4.4 6.5 - - + -
243B GLY* 3.6 22.8 - - - +
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Residues in contact with VAL 27 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A ILE* 3.6 26.2 - - + -
13B VAL* 4.6 9.2 - - + -
15B VAL* 4.3 15.7 - - + -
23B CYS* 2.8 26.1 + - + +
24B ALA 3.8 4.3 - - - +
26B VAL* 1.3 72.4 - - - +
28B LYS* 1.3 62.5 - - - +
30B ILE* 3.1 9.9 + - + +
31B GLU* 2.9 40.9 + - + +
41B ILE* 5.1 2.7 - - + -
43B LEU* 4.0 29.4 - - + -
71B MET* 4.9 2.9 - - - -
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Residues in contact with LYS 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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24B ALA 3.0 14.4 + - - +
25B ALA* 3.5 13.2 - - - +
26B VAL 3.2 0.4 - - - -
27B VAL* 1.3 76.3 - - - +
29B GLY* 1.3 57.2 + - - +
31B GLU* 3.4 17.1 + - - +
32B LYS* 3.1 38.4 + - + +
240B GLU* 3.5 26.9 - - - +
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Residues in contact with GLY 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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25B ALA 3.4 4.6 + - - -
26B VAL 3.0 5.5 + - - -
28B LYS* 1.3 75.8 - - - +
30B ILE* 1.3 68.8 + - - +
32B LYS* 3.2 2.1 + - - -
33B THR 3.2 16.5 + - - -
240B GLU* 3.4 34.7 - - - +
244B MET* 3.4 22.5 - - - +
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Residues in contact with ILE 30 (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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13B VAL* 3.8 37.5 - - + -
26B VAL* 2.9 32.4 + - + +
27B VAL* 3.5 10.8 - - + +
29B GLY* 1.3 78.3 - - - +
31B GLU* 1.3 56.8 + - - +
33B THR 3.3 0.2 + - - -
34B ALA* 2.8 30.7 + - - +
41B ILE* 3.6 26.7 - - + -
69B ILE* 4.1 23.3 - - + -
71B MET* 5.6 0.7 - - - -
92B CYS* 4.9 0.2 - - - -
243B GLY* 3.5 18.6 - - - +
247B VAL* 3.4 20.8 - - + +
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Residues in contact with GLU 31 (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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45A ASN* 3.0 39.8 + - - +
47A GLU* 4.6 2.6 - - - +
52A ARG* 3.8 29.7 + - - +
27B VAL* 2.9 30.0 + - + +
28B LYS* 3.6 20.7 + - - +
29B GLY 3.2 0.2 - - - -
30B ILE* 1.3 71.9 - - - +
32B LYS* 1.3 67.9 + - + +
35B GLU* 3.0 34.0 + - - +
41B ILE* 4.1 27.2 - - + +
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Residues in contact with LYS 32 (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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28B LYS* 3.1 28.8 + - - +
29B GLY 3.7 7.0 - - - +
30B ILE 3.2 0.4 - - - -
31B GLU* 1.3 79.7 - - + +
33B THR* 1.3 65.0 + - - +
35B GLU* 4.4 1.9 - - - +
36B LYS* 3.6 24.3 + - - +
240B GLU* 2.7 36.8 + - + +
244B MET* 4.0 18.5 - - + -
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Residues in contact with THR 33 (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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29B GLY 3.2 6.9 + - - -
32B LYS* 1.3 77.3 - - - +
34B ALA* 1.3 63.3 + - - +
36B LYS* 3.4 9.2 + - + +
37B ASN* 2.9 37.3 + - - +
244B MET* 3.3 39.7 - - - +
247B VAL* 3.6 23.1 - - + -
248B SER* 4.2 11.0 - - - +
251B LEU* 4.4 2.9 - - + -
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Residues in contact with ALA 34 (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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11B LEU* 3.9 16.8 - - + -
30B ILE 2.8 21.6 + - - +
31B GLU 4.2 0.7 - - - +
33B THR* 1.3 70.7 - - - +
35B GLU* 1.3 58.1 + - - +
37B ASN* 3.0 20.9 + - - +
38B GLY 3.3 0.2 + - - -
39B TYR* 3.0 28.2 + - + +
41B ILE* 3.5 31.0 - - + -
247B VAL* 3.8 11.1 - - + +
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Residues in contact with GLU 35 (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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49A ASP* 5.6 0.2 - - - +
52A ARG* 2.8 40.7 + - - +
31B GLU* 3.0 26.2 + - - +
32B LYS* 4.5 1.7 - - - +
34B ALA* 1.3 76.0 - - + +
36B LYS* 1.3 59.6 + - - +
37B ASN 3.2 1.5 + - - -
38B GLY* 4.0 7.0 + - - -
39B TYR 3.2 17.3 - - - +
40B ARG* 2.8 45.8 + - - +
41B ILE* 5.2 2.7 + - + +
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Residues in contact with LYS 36 (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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32B LYS 3.6 15.4 + - - +
33B THR* 3.4 10.7 + - - +
34B ALA 3.2 0.2 - - - -
35B GLU* 1.3 78.0 - - - +
37B ASN* 1.3 66.5 + - - +
38B GLY 3.6 0.9 - - - -
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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