Contacts of the helix formed by residues 26 - 37 (chain B) in PDB entry 1JWG
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 ASP 26 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16B ARG* 4.2 14.5 - - - +
17B ALA* 4.8 3.1 + - - -
22B ASN* 4.1 23.6 + - - +
24B GLU 3.2 3.8 + - - +
25B LEU* 1.3 68.7 - - - +
27B TRP* 1.3 57.2 + - - +
28B ALA* 3.5 10.0 + - - +
29B SER* 2.5 37.5 + - - -
30B ILE* 2.8 33.6 + - - +
65B GLN* 4.8 1.4 - - - +
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Residues in contact with TRP 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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25B LEU* 3.3 48.6 + - + +
26B ASP* 1.3 73.3 + - - +
28B ALA* 1.3 54.4 - - - +
30B ILE* 3.5 20.1 - - + +
31B ASN* 2.7 53.2 + - - +
68B THR* 3.8 16.8 - - + -
72B THR* 3.5 27.4 - - + -
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Residues in contact with ALA 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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13B ARG* 5.3 1.0 + - - -
26B ASP* 3.3 8.2 + - - +
27B TRP* 1.3 77.6 - - - +
29B SER* 1.3 59.4 + - - +
31B ASN* 3.9 5.0 - - - +
32B GLY* 3.0 23.6 + - - -
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Residues in contact with SER 29 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B ARG* 4.4 6.8 - - - +
16B ARG* 3.5 31.8 + - - +
17B ALA* 3.9 25.0 - - - +
26B ASP* 2.5 36.0 + - - -
28B ALA* 1.3 76.0 - - - +
30B ILE* 1.3 65.2 + - - +
32B GLY* 3.3 1.6 + - - -
33B PHE* 3.1 23.7 + - - +
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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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17B ALA* 4.0 15.3 - - + +
25B LEU* 4.2 23.1 - - + -
26B ASP 2.8 25.0 + - - +
27B TRP* 3.5 33.9 - - + +
29B SER* 1.3 78.8 - - - +
31B ASN* 1.3 62.0 + - - +
33B PHE* 3.2 11.3 + - - +
34B CYS* 3.2 13.9 + - - -
65B GLN 5.3 0.4 - - - +
68B THR* 4.2 7.4 - - + -
69B VAL* 3.7 29.7 - - + +
72B THR* 3.8 34.3 - - + +
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Residues in contact with ASN 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 TRP* 2.7 36.4 + - - +
28B ALA* 4.1 4.7 - - - +
30B ILE* 1.3 74.4 - - - +
32B GLY* 1.3 59.5 + - - +
34B CYS* 3.2 7.3 + - - +
35B GLU* 2.8 36.0 + - + +
72B THR* 3.8 25.3 - - - +
76B SER* 5.1 3.6 + - - -
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Residues in contact with GLY 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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13B ARG* 3.2 37.0 + - - -
28B ALA 3.0 17.4 + - - -
29B SER 3.3 2.2 + - - -
31B ASN* 1.3 75.8 - - - +
33B PHE* 1.3 61.5 + - - +
35B GLU* 3.4 8.9 + - - +
36B GLN* 3.1 17.8 + - - +
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Residues in contact with PHE 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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10B LEU* 3.7 38.1 - - + +
13B ARG* 4.0 13.9 - - + +
14B ILE* 3.6 36.8 - - + -
17B ALA* 5.1 1.1 - - + -
29B SER 3.1 12.4 + - - +
30B ILE* 3.4 9.9 - - - +
31B ASN 3.1 0.2 - - - -
32B GLY* 1.3 74.5 - - - +
34B CYS* 1.3 65.2 + - - +
36B GLN* 3.1 10.9 + - - +
37B LEU* 3.2 15.2 + - + +
47B ALA* 3.7 37.9 - - + -
50B LEU* 4.4 4.0 - - + -
51B LEU* 4.0 14.8 - - + -
69B VAL* 3.6 27.6 - - + -
73B CYS* 3.7 10.1 - - - -
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Residues in contact with CYS 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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77A CYS* 3.5 14.5 - - + +
30B ILE* 3.2 14.7 + - - +
31B ASN* 3.6 10.3 - - - +
33B PHE* 1.3 78.8 - - - +
35B GLU* 1.3 63.4 + - + +
36B GLN 3.3 0.9 + - - -
37B LEU* 3.4 18.9 + - - +
38B ASN* 3.7 1.0 - - - +
69B VAL* 4.2 0.9 - - - -
72B THR* 3.8 15.3 - - + -
73B CYS* 2.1 66.0 - - + -
76B SER* 4.6 10.3 - - - +
77B CYS* 4.3 5.2 - - - -
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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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77A CYS* 3.4 8.8 - - - +
78A GLY 3.0 22.5 + - - +
79A LYS* 2.9 50.0 + - + +
82A HIS* 2.7 35.6 + - - +
126A LEU* 5.3 3.6 - - - -
128A GLU* 5.0 9.5 - - - +
129A GLU* 5.5 0.3 - - - +
31B ASN* 2.8 23.8 + - + +
32B GLY* 3.7 9.4 - - - +
33B PHE 3.1 0.2 - - - -
34B CYS* 1.3 79.3 - - + +
36B GLN* 1.3 57.9 + - - +
38B ASN* 3.6 7.0 - - - +
148B IOD 3.7 2.4 - - - +
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Residues in contact with GLN 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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79A LYS* 3.8 21.4 - - - +
8B GLU* 3.5 28.1 + - - +
9B THR* 5.3 0.2 - - - -
10B LEU* 3.6 23.5 - - + +
13B ARG* 3.7 20.1 + - - +
32B GLY 3.1 15.4 + - - +
33B PHE 3.1 1.0 + - - +
35B GLU* 1.3 76.2 - - - +
37B LEU* 1.3 65.2 + - - +
38B ASN 3.3 3.1 - - - -
39B GLU* 3.1 57.6 + - - +
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Residues in contact with LEU 37 (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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10B LEU* 4.0 11.2 - - + -
33B PHE* 3.2 10.7 + - + +
34B CYS* 3.4 14.1 - - - +
35B GLU 3.6 0.4 - - - -
36B GLN* 1.3 77.7 - - - +
38B ASN* 1.3 71.0 + - + +
39B GLU 3.3 1.3 + - - -
43B GLY* 3.1 28.1 - - - +
44B PRO* 3.2 11.8 - - + +
47B ALA* 3.9 22.2 - - + -
73B CYS* 3.9 16.8 - - - -
77B CYS* 3.8 22.7 - - - -
81B PHE* 3.7 43.5 - - + -
151B IOD 4.2 4.5 - - + -
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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