Contacts of the helix formed by residues 15 - 32 (chain B) in PDB entry 4J6V
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 THR 15 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9B LYS* 6.1 0.2 - - - +
13B HIS 3.8 3.8 + - - +
14B LEU* 1.3 80.1 - - - +
16B ASP* 1.3 64.7 + - - +
17B THR* 3.6 8.3 + - - -
18B GLU* 2.9 41.6 + - - +
19B LYS* 3.4 15.8 + - - +
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Residues in contact with ASP 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 THR* 1.3 73.2 - - - +
17B THR* 1.3 67.5 + - - +
19B LYS* 2.8 29.3 + - - +
20B ARG* 3.1 13.0 + - - +
112B ASP* 4.0 16.0 - - - +
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Residues in contact with THR 17 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B THR* 4.0 7.4 - - - -
16B ASP* 1.3 81.2 - - - +
18B GLU* 1.3 63.1 + - + +
20B ARG* 3.4 7.9 + - + +
21B ASP* 3.0 40.3 + - - +
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Residues in contact with GLU 18 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B LYS* 3.0 31.9 + - - +
13B HIS 4.4 1.0 - - - +
14B LEU* 3.6 27.3 - - + +
15B THR* 2.9 51.6 + - - +
16B ASP 3.0 0.2 + - - -
17B THR* 1.3 77.6 - - + +
19B LYS* 1.3 57.8 + - - +
21B ASP* 3.5 5.9 + - - +
22B PHE* 2.9 27.9 + - - +
86B GLU 5.7 1.7 - - - +
87B VAL* 5.8 0.2 - - - +
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Residues in contact with LYS 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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11B VAL* 4.0 20.8 + - - +
12B LEU* 5.8 2.4 + - - +
14B LEU* 3.7 26.8 + - + -
15B THR 3.6 11.0 - - - +
16B ASP* 2.8 21.4 + - - +
18B GLU* 1.3 70.9 - - - +
20B ARG* 1.3 58.5 + - - +
21B ASP 3.1 1.8 - - - -
22B PHE* 4.0 1.2 - - - +
23B VAL* 3.0 35.6 + - - +
107B GLN* 4.4 25.9 + - - +
110B SER* 4.7 3.0 + - - -
112B ASP* 3.9 28.1 + - - +
113B PHE* 3.6 35.2 - - + -
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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 ASP 3.1 9.1 + - - +
17B THR* 3.9 10.5 - - - +
19B LYS* 1.3 79.3 - - - +
21B ASP* 1.3 73.0 + - - +
23B VAL* 4.2 4.0 - - - +
24B ARG* 3.1 58.0 + - - +
112B ASP 5.0 4.5 - - - -
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Residues in contact with ASP 21 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17B THR* 3.0 35.6 + - - +
18B GLU* 3.7 6.1 - - - +
20B ARG* 1.3 82.9 - - - +
22B PHE* 1.3 61.2 + - - +
24B ARG* 2.5 44.6 + - - +
25B THR* 2.7 33.9 + - - -
84B ASN* 4.4 4.3 + - - -
87B VAL* 4.3 13.2 - - + -
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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
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14B LEU* 6.3 0.4 - - + -
18B GLU 2.9 18.0 + - - +
19B LYS* 4.0 5.8 - - - +
21B ASP* 1.3 76.6 - - - +
23B VAL* 1.3 65.7 + - - +
25B THR* 3.2 3.8 + - - -
26B VAL* 2.9 44.8 + - + +
76B PHE* 5.0 4.3 - + - -
80B LEU* 3.9 22.0 - - + -
87B VAL* 4.0 19.0 - - + +
88B THR 3.9 8.3 - - - +
89B LEU* 4.2 7.0 - - + -
90B PRO* 3.5 27.4 - - + -
113B PHE* 3.9 18.4 - + + -
114B MET* 4.0 20.9 - - + -
225B PRO* 5.5 4.7 - - + -
228B PHE* 5.6 1.6 - - + -
229B LEU* 4.0 24.0 - - + -
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Residues in contact with VAL 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 LYS 3.0 20.2 + - - +
20B ARG* 4.2 4.3 - - - +
22B PHE* 1.3 78.9 - - - +
24B ARG* 1.3 57.5 - - - +
26B VAL* 3.3 7.1 + - - +
27B LEU* 3.0 36.4 + - + +
112B ASP 4.0 7.6 - - - +
113B PHE* 3.5 38.6 - - + +
114B MET* 4.3 3.4 - - + -
130B PRO* 3.5 30.3 - - + -
131B PHE* 4.2 11.8 - - + -
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Residues in contact with ARG 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 ARG* 3.1 56.8 + - - +
21B ASP* 2.5 44.1 + - - +
23B VAL* 1.3 78.8 - - - +
25B THR* 1.3 63.4 + - - +
27B LEU* 3.4 12.1 + - + +
28B ILE* 3.1 37.0 + - + +
84B ASN* 3.1 24.2 - - - +
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Residues in contact with THR 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 ASP 2.7 22.6 + - - -
22B PHE 3.2 4.2 + - - -
24B ARG* 1.3 77.7 + - - +
26B VAL* 1.3 64.6 + - - +
28B ILE* 3.2 9.7 + - - +
29B LEU* 3.1 22.4 + - + +
80B LEU* 3.5 45.5 - - + +
83B ILE* 3.7 19.0 - - + +
84B ASN* 3.9 9.7 + - + +
87B VAL* 3.5 16.8 - - + +
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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
----------------------------------------------------------
22B PHE* 2.9 50.1 + - + +
23B VAL* 3.3 9.2 + - - +
25B THR* 1.3 78.6 - - - +
27B LEU* 1.3 61.2 + - - +
29B LEU* 3.3 8.6 + - - +
30B LYS* 3.1 20.6 + - - +
35B TYR* 4.0 16.6 - - + -
76B PHE* 4.5 7.0 - - + -
80B LEU* 4.2 11.9 - - + -
131B PHE* 4.1 15.7 - - + -
136B TRP* 3.9 22.9 - - + -
225B PRO* 4.5 6.3 - - + -
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Residues in contact with LEU 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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23B VAL* 3.0 36.0 + - + +
24B ARG* 3.7 9.9 - - + +
25B THR 3.2 0.4 - - - -
26B VAL* 1.3 75.9 - - - +
28B ILE* 1.3 57.2 + - + +
30B LYS* 3.4 5.4 + - + +
31B GLU* 3.0 28.6 + - - +
130B PRO* 4.0 21.3 - - + +
131B PHE* 4.1 7.0 - - + -
135B ARG 4.4 8.7 - - - +
136B TRP* 3.9 26.5 - - + -
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Residues in contact with ILE 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 ARG* 3.1 35.4 + - + +
25B THR* 3.5 7.6 - - - +
26B VAL 3.2 0.2 - - - -
27B LEU* 1.3 76.2 - - + +
29B LEU* 1.3 60.7 + - - +
31B GLU* 3.3 6.8 + - - +
32B LYS* 2.9 57.8 + - + +
83B ILE* 3.7 34.1 - - + -
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Residues in contact with LEU 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 THR 3.1 11.9 + - - +
26B VAL* 3.3 9.6 + - - +
28B ILE* 1.3 76.8 - - - +
30B LYS* 1.3 60.2 + - - +
32B LYS* 3.5 3.0 + - - -
33B GLY 3.4 2.9 + - - -
34B ILE* 3.0 54.3 + - + +
35B TYR* 3.1 10.7 + - + +
38B TYR* 5.1 0.4 - - + -
76B PHE* 3.9 28.5 - - + -
79B ASP* 3.6 35.4 - - + +
80B LEU* 4.3 12.3 - - + +
82B SER* 5.4 0.2 - - - +
83B ILE* 3.4 35.9 - - + -
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Residues in contact with LYS 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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26B VAL 3.1 7.2 + - - +
27B LEU* 3.6 8.3 - - + +
28B ILE 3.2 0.2 - - - -
29B LEU* 1.3 75.4 - - - +
31B GLU* 1.3 65.8 + - - +
33B GLY* 3.3 12.5 + - - -
35B TYR* 3.6 18.8 - - + +
36B ASP* 4.2 21.3 + - - +
39B ILE* 4.1 23.4 - - - +
136B TRP* 3.5 50.3 - - + -
137B THR* 2.8 38.8 + - - +
138B THR* 4.6 3.4 - - - +
139B ILE* 5.3 0.8 - - - +
223B ASN* 4.6 0.8 + - - -
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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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27B LEU 3.0 17.9 + - - +
28B ILE* 3.3 7.1 + - - +
30B LYS* 1.3 78.8 - - - +
32B LYS* 1.3 74.8 + - - +
33B GLY 3.4 0.9 + - - -
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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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258A PHE* 3.4 29.5 - - + +
28B ILE* 2.9 42.9 + - + +
29B LEU* 4.1 4.0 - - - +
30B LYS 3.3 0.2 - - - -
31B GLU* 1.3 87.3 - - - +
33B GLY* 1.3 58.1 + - - +
34B ILE* 3.3 18.1 + - + -
83B ILE* 3.9 17.5 - - + -
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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