Contacts of the helix formed by residues 17 - 33 (chain B) in PDB entry 1W1J
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 SER 17 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12B LEU* 4.2 1.7 - - - +
15B LYS 3.9 2.8 + - - -
16B LEU* 1.3 80.9 - - - +
18B LEU* 1.3 63.4 + - - +
19B SER* 3.6 12.4 + - - -
20B ASP* 3.3 28.3 + - - +
21B PHE* 3.3 18.0 + - - +
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Residues in contact with LEU 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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7B PHE 4.7 3.8 - - - +
8B ARG* 4.7 15.3 - - + -
9B PRO* 4.0 24.9 - - + +
12B LEU* 3.9 26.6 - - + +
17B SER* 1.3 70.5 - - - +
19B SER* 1.3 66.5 + - - +
21B PHE* 3.2 3.9 + - + +
22B ASN* 3.1 40.5 + - - +
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Residues in contact with SER 19 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17B SER* 3.6 10.9 - - - -
18B LEU* 1.3 78.1 - - - +
20B ASP* 1.3 60.3 + - - +
22B ASN* 3.2 9.6 + - - +
23B GLU* 3.0 27.6 + - - +
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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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16B LEU* 3.8 26.7 - - + +
17B SER* 3.3 23.9 + - - +
18B LEU 3.2 0.8 - - - -
19B SER* 1.3 74.2 + - - +
21B PHE* 1.3 57.0 + - - +
22B ASN 2.8 1.9 + - - -
23B GLU* 3.0 11.4 + - - +
24B PHE* 2.7 37.7 + - - +
93B PHE* 3.9 23.5 - - + -
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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
----------------------------------------------------------
6B GLU 4.4 8.3 - - - -
9B PRO* 3.6 33.7 - - + -
12B LEU* 3.6 28.9 - - + -
13B PRO* 4.2 3.1 - - + -
16B LEU* 4.1 8.1 - - + +
17B SER 3.3 4.5 + - - +
18B LEU 3.2 9.3 + - - +
20B ASP* 1.3 76.2 - - - +
22B ASN* 1.3 65.0 + - - +
24B PHE* 3.5 7.1 - - - +
25B ILE* 3.0 47.7 + - + +
39B VAL* 4.0 15.3 - - + -
72B SER* 3.2 41.3 - - - -
95B PHE* 3.7 20.6 - + - -
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Residues in contact with ASN 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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6B GLU 3.3 20.5 + - - +
7B PHE* 2.7 30.1 + - - +
18B LEU* 3.1 30.1 + - - +
19B SER* 3.4 10.5 - - - +
20B ASP 2.8 1.6 + - - -
21B PHE* 1.3 79.3 - - - +
23B GLU* 1.3 56.4 - - - +
24B PHE 2.9 4.3 - - - -
25B ILE* 4.4 3.8 - - - +
26B GLN* 2.9 39.1 + - - +
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Residues in contact with GLU 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 SER* 3.0 15.2 + - - +
20B ASP* 3.0 13.1 + - - +
22B ASN* 1.3 74.6 - - - +
24B PHE* 1.3 55.3 + - - +
26B GLN* 4.2 8.0 - - + +
27B ASP* 2.8 37.6 + - - +
92B LYS* 5.5 4.0 + - - -
93B PHE* 4.1 24.4 - - + -
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Residues in contact with PHE 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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16B LEU* 5.8 0.4 - - + -
20B ASP 2.7 18.3 + - - +
21B PHE* 3.5 7.4 - - - +
23B GLU* 1.3 77.0 - - - +
25B ILE* 1.3 68.8 + - + +
26B GLN 3.1 1.3 - - - -
27B ASP* 2.8 22.8 + - - +
28B ILE* 2.9 45.3 + - + +
86B ILE 4.9 0.9 - - - -
89B LEU* 3.7 11.4 - - + -
90B ALA* 3.7 26.7 - - + -
93B PHE* 3.4 30.7 - + + -
95B PHE* 3.3 50.0 - + + -
97B LEU* 5.1 4.0 - - + -
119B VAL* 4.1 13.7 - - + -
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Residues in contact with ILE 25 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6B GLU 3.3 34.3 - - - +
21B PHE* 3.0 50.7 + - + +
22B ASN* 4.4 3.6 - - - +
24B PHE* 1.3 93.9 - - + +
26B GLN* 1.3 58.7 + - - +
28B ILE* 3.8 7.7 - - + +
29B ILE* 2.9 38.9 + - + +
37B VAL* 4.2 13.0 - - + -
39B VAL* 4.2 13.7 - - + -
73B ALA* 3.7 18.6 - - + -
75B VAL* 5.6 0.9 - - + -
95B PHE* 4.5 2.5 - - + -
119B VAL* 4.7 1.1 - - + -
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Residues in contact with GLN 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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6B GLU 4.4 16.6 - - - +
22B ASN* 2.9 26.0 + - - +
23B GLU* 4.3 8.7 - - + +
25B ILE* 1.3 80.1 - - - +
27B ASP* 1.3 56.5 + - - +
29B ILE* 3.6 17.9 + - - +
30B ARG* 3.2 47.2 + - - +
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Residues in contact with ASP 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 GLU* 2.8 30.2 - - - +
24B PHE 2.8 9.8 + - - +
26B GLN* 1.3 75.5 - - - +
28B ILE* 1.3 63.9 + - - +
30B ARG* 3.0 25.6 + - - +
31B ILE* 3.4 27.4 + - - +
89B LEU* 3.8 29.2 - - + +
93B PHE* 4.4 5.2 - - - -
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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
----------------------------------------------------------
24B PHE* 2.9 50.8 + - + +
25B ILE* 3.8 8.3 - - + +
27B ASP* 1.3 74.5 - - - +
29B ILE* 1.3 59.4 + - - +
30B ARG 3.2 0.2 - - - -
31B ILE* 3.2 5.2 + - - +
32B VAL* 2.9 37.1 + - + +
37B VAL* 4.0 10.5 - - + -
75B VAL* 3.6 39.9 - - + -
86B ILE* 3.7 31.2 - - + -
89B LEU* 4.1 14.8 - - + -
119B VAL* 5.8 0.9 - - + -
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Residues in contact with ILE 29 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6B GLU* 4.3 11.4 - - + +
25B ILE* 2.9 38.9 + - + +
26B GLN* 3.9 22.9 - - - +
27B ASP 3.4 0.2 - - - -
28B ILE* 1.3 75.6 - - - +
30B ARG* 1.3 61.3 + - + +
33B GLY* 2.9 28.1 + - - +
34B SER* 3.8 28.7 - - - +
37B VAL* 3.7 30.3 - - + +
39B VAL* 5.7 0.4 - - + -
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Residues in contact with ARG 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 GLN* 3.2 41.5 + - - +
27B ASP* 3.0 34.5 + - - +
28B ILE 3.2 0.2 - - - -
29B ILE* 1.3 81.2 - - - +
31B ILE* 1.3 63.2 + - + +
33B GLY 4.6 0.7 + - - -
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Residues in contact with ILE 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 ASP* 3.4 16.3 + - + +
28B ILE* 3.2 7.4 + - - +
30B ARG* 1.3 80.8 - - + +
32B VAL* 1.3 70.5 + - + +
33B GLY 3.5 0.5 + - - -
78B ARG* 3.5 17.8 + - - +
82B ASP* 3.7 29.4 - - + +
85B SER* 3.6 34.8 - - - +
86B ILE* 4.8 2.7 - - + +
89B LEU* 3.7 20.6 - - + -
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Residues in contact with VAL 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 ILE* 2.9 29.2 + - + +
31B ILE* 1.3 85.4 - - + +
33B GLY* 1.3 72.5 + - - +
35B GLU* 5.6 0.5 - - - +
36B ASN* 3.5 35.4 + - + +
37B VAL* 3.4 20.2 - - + -
75B VAL* 4.2 15.5 - - + -
76B ALA 4.4 2.9 - - - +
77B PRO* 4.5 4.3 - - + -
78B ARG* 3.8 16.9 - - + +
82B ASP* 4.1 17.7 - - + +
86B ILE* 4.4 8.5 - - + -
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Residues in contact with GLY 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 ILE* 2.9 19.5 + - - -
30B ARG 4.5 0.8 + - - -
31B ILE 3.4 2.8 + - - -
32B VAL* 1.3 87.8 - - - +
34B SER* 1.3 58.9 + - - -
35B GLU* 3.0 7.9 - - - -
36B ASN 3.0 17.8 + - - -
37B VAL* 3.8 1.6 - - - +
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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
------------------------------------------------------------
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