Contacts of the helix formed by residues 15 - 33 (chain V) in PDB entry 5JPQ
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 PRO 15 (chain V).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13V GLU 4.0 3.6 - - - -
14V VAL* 1.3 72.4 - - - +
16V GLN* 1.3 59.3 + - - +
17V ASP* 3.1 7.4 - - + +
18V LEU* 2.9 29.8 + - + +
19V ALA 3.1 8.0 + - - -
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Residues in contact with GLN 16 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14V VAL 3.7 1.8 + - - -
15V PRO* 1.3 71.7 - - - +
17V ASP* 1.3 60.2 + - - +
19V ALA* 3.6 12.4 - - + +
20V ASP* 3.0 24.6 + - - +
342Y ARG* 5.5 7.1 - - + +
399Y GLU 4.7 5.4 - - - +
400Y GLY* 4.6 24.5 - - - +
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Residues in contact with ASP 17 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15V PRO* 3.0 5.7 + - + +
16V GLN* 1.3 76.6 - - - +
18V LEU* 1.3 59.3 + - - +
20V ASP* 3.4 7.1 + - - +
21V LYS* 3.0 26.6 + - - +
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Residues in contact with LEU 18 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14V VAL* 5.2 5.6 - - + -
15V PRO* 2.9 19.0 + - + +
17V ASP* 1.3 78.3 - - - +
19V ALA* 1.3 59.3 + - - +
21V LYS* 3.0 9.0 + - - +
22V VAL* 2.8 30.8 + - - +
117V ILE* 6.2 0.5 - - - +
120V ARG* 5.8 8.1 - - + -
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Residues in contact with ALA 19 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14V VAL* 5.1 8.3 - - + +
15V PRO 3.1 5.9 + - - +
16V GLN* 3.6 18.2 - - - +
18V LEU* 1.3 78.6 - - - +
20V ASP* 1.3 57.1 + - - +
22V VAL* 3.5 7.6 + - - +
23V LEU* 3.2 24.6 + - - +
82V TYR 4.5 16.2 - - - +
83V VAL* 4.7 16.0 - - + +
84V SER* 5.2 4.5 - - - +
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Residues in contact with ASP 20 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16V GLN 3.0 17.1 + - - +
17V ASP* 3.7 6.1 - - - +
19V ALA* 1.3 73.8 - - - +
21V LYS* 1.3 61.3 + - - +
22V VAL 3.2 0.7 - - - -
23V LEU* 3.5 5.8 + - - +
24V GLU* 3.0 29.2 + - - +
342Y ARG* 5.9 8.1 - - + +
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Residues in contact with LYS 21 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17V ASP 3.0 14.3 + - - +
18V LEU* 3.0 11.4 + - - +
20V ASP* 1.3 76.0 - - - +
22V VAL* 1.3 57.6 + - - +
24V GLU* 3.8 7.1 - - - +
25V ALA* 3.1 25.8 + - - +
113V LEU* 5.4 5.5 - - - +
117V ILE* 5.9 6.4 - - + +
184u SER 3.9 2.3 - - - +
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Residues in contact with VAL 22 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18V LEU 2.8 11.9 + - - +
19V ALA* 3.6 11.9 - - - +
20V ASP 3.2 0.2 - - - -
21V LYS* 1.3 74.9 - - - +
23V LEU* 1.3 66.3 + - - +
25V ALA* 2.9 18.3 + - - +
26V VAL* 2.9 13.6 + - - +
55V ILE* 5.9 6.7 - - + -
81V VAL* 5.3 11.4 - - + -
82V TYR 5.2 6.7 - - - +
83V VAL* 5.8 4.0 - - + -
117V ILE* 5.8 8.9 - - + +
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Residues in contact with LEU 23 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19V ALA 3.2 13.6 + - - +
20V ASP* 3.5 6.5 + - - +
22V VAL* 1.3 74.1 - - - +
24V GLU* 1.3 50.3 - - - +
26V VAL* 4.6 3.8 - - - -
27V ARG* 3.9 1.4 - - - +
83V VAL* 6.2 3.3 - - + +
88V ALA* 5.4 5.2 - - + +
89V LEU* 6.1 1.8 - - - -
92V ALA* 4.2 16.3 - - + +
183u ALA* 1.4 44.2 - - - +
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Residues in contact with GLU 24 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20V ASP 3.0 17.5 + - - +
21V LYS* 3.8 7.6 - - - +
23V LEU* 1.3 72.0 - - - +
25V ALA 1.3 46.2 - - - +
27V ARG* 4.7 1.6 - - - -
182u GLU 2.6 2.7 - - - +
183u ALA* 1.3 25.3 - - - +
184u SER 1.2 64.2 + - - +
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Residues in contact with ALA 25 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21V LYS 3.1 12.2 + - - +
22V VAL* 2.9 13.3 + - - +
24V GLU* 1.3 67.0 - - - +
26V VAL* 1.3 43.6 + - - +
29V ALA* 3.2 15.9 + - - +
110V ALA* 3.9 4.7 - - + +
113V LEU* 4.7 7.2 - - + +
114V VAL* 4.9 13.0 - - + +
117V ILE* 6.1 2.5 - - + -
183u ALA 0.9 42.2 - - - +
184u SER* 2.5 29.0 + - - +
185u GLY 4.2 0.9 - - - +
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Residues in contact with VAL 26 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22V VAL 2.9 10.6 + - - +
23V LEU* 3.6 3.6 - - - +
25V ALA* 1.3 65.5 - - - +
27V ARG* 1.3 48.4 + - - -
29V ALA* 3.0 9.0 + - - +
30V LYS* 3.0 21.7 + - - +
35V ILE* 5.3 2.8 - - - +
89V LEU 6.0 0.2 - - - +
92V ALA* 4.9 8.5 - - + -
93V CYS* 5.7 4.9 - - - +
102V ALA* 6.3 2.7 - - + -
181u ALA* 2.6 12.0 - - - +
183u ALA* 1.4 34.1 + - + +
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Residues in contact with ARG 27 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23V LEU 3.9 1.1 - - - +
24V GLU* 4.7 1.3 - - - -
26V VAL 1.3 57.5 - - - -
28V LYS* 1.3 57.4 + - - -
30V LYS* 3.2 6.2 + - - +
31V GLU 3.3 5.9 + - - -
92V ALA* 4.7 2.9 - - + +
179u ARG 4.1 1.6 - - - +
181u ALA* 1.5 29.8 - - - +
182u GLU* 1.5 77.1 + - + +
183u ALA* 1.1 155.3 - - + +
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Residues in contact with LYS 28 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27V ARG 1.3 68.8 - - - -
29V ALA* 1.3 55.6 + - - +
31V GLU* 3.4 2.5 + - - +
32V SER* 2.9 33.1 + - - -
107V PRO 4.6 1.6 - - - +
109V GLU 3.9 2.2 - - - +
115u LYS* 3.7 21.1 - - - +
117u GLY 4.6 1.5 + - - +
182u GLU* 1.6 28.6 + - - +
183u ALA 2.2 4.0 - - - +
184u SER* 1.5 54.5 - - - -
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Residues in contact with ALA 29 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25V ALA 3.2 15.1 + - - +
26V VAL* 3.0 12.6 + - - +
28V LYS* 1.3 76.7 - - - +
30V LYS* 1.3 63.8 + - - +
33V GLY 3.0 29.7 + - - +
34V LYS* 3.5 3.8 + - - +
35V ILE* 4.9 10.3 - - + -
104V ILE* 4.9 13.2 - - + -
106V GLU 4.4 8.3 - - - +
107V PRO* 4.0 21.5 - - + +
184u SER* 3.7 0.2 - - - -
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Residues in contact with LYS 30 (chain V).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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26V VAL 3.0 8.0 + - - +
27V ARG 3.2 1.3 + - - +
29V ALA* 1.3 77.5 - - - +
31V GLU* 1.3 64.2 + - - +
33V GLY 3.9 7.5 - - - +
35V ILE* 5.0 8.7 - - + +
93V CYS* 4.7 3.8 - - - +
178u ALA* 4.2 9.3 - - - +
181u ALA* 3.2 37.2 - - + +
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Residues in contact with GLU 31 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27V ARG 3.3 6.4 + - - +
28V LYS 3.6 6.3 - - - +
29V ALA 3.3 0.2 - - - -
30V LYS* 1.3 85.1 - - - +
32V SER* 1.3 61.6 + - - +
33V GLY 4.9 0.5 - - - +
114u TYR 5.1 0.2 - - - +
117u GLY* 2.8 46.4 - - - +
119u ALA 5.5 0.4 - - - +
120u LYS* 5.4 2.9 - - - +
178u ALA* 4.4 16.3 - - + +
179u ARG* 4.5 0.2 - - - -
182u GLU* 4.2 0.4 - - + -
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Residues in contact with SER 32 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28V LYS 2.9 13.8 + - - -
31V GLU* 1.3 78.8 - - - +
33V GLY* 1.3 58.7 + - - +
108V GLY* 4.0 8.8 - - - -
109V GLU* 3.7 32.1 - - - -
114u TYR 5.0 5.4 - - - -
120u LYS 5.8 4.5 - - - -
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Residues in contact with GLY 33 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28V LYS 4.1 0.4 + - - -
29V ALA* 3.0 18.2 + - - +
30V LYS 3.9 8.3 - - - +
31V GLU 4.9 0.5 - - - +
32V SER* 1.3 81.7 - - - +
34V LYS* 1.3 61.2 + - - +
35V ILE 4.5 0.2 + - - -
106V GLU* 3.4 17.7 - - - -
108V GLY* 4.4 5.6 - - - -
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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