Contacts of the helix formed by residues 18 - 31 (chain B) in PDB entry 1W2I
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 GLY 18 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16B GLY 3.7 1.6 - - - -
17B VAL* 1.3 77.5 - - - +
19B PHE* 1.3 58.3 + - - +
21B TRP* 3.5 18.8 + - - +
22B SER* 2.9 36.5 + - - -
66B PRO* 4.0 0.7 - - - -
1092B FMT 3.1 22.3 + - - -
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Residues in contact with PHE 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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10B ILE* 3.9 33.2 - - + -
14B VAL* 3.3 32.5 - - + +
15B GLN* 5.5 0.2 - - - -
17B VAL* 3.3 6.4 - - + +
18B GLY* 1.3 77.2 - - - +
20B ARG* 1.3 60.3 + - + +
22B SER* 3.8 0.5 - - - -
23B MET* 2.8 40.9 + - + +
44B VAL* 4.3 18.6 - - + -
61B TRP* 4.1 10.2 - + - -
62B ALA* 3.6 18.6 - - - -
65B GLY* 4.1 10.8 - - - -
66B PRO* 3.7 20.0 - - + -
69B ALA* 3.9 9.6 - - + -
71B VAL* 3.8 23.3 - - + -
1092B FMT 3.2 3.0 + - - +
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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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19B PHE* 1.3 73.6 - - + +
21B TRP* 1.3 75.3 + - - +
23B MET* 3.4 1.7 + - - +
24B GLN* 3.0 25.1 + - - +
36B VAL* 4.0 27.2 - - + +
37B ARG* 4.3 1.3 - - - +
38B ASN* 3.4 39.0 + - - +
44B VAL* 5.2 1.8 - - + -
89B ILE* 3.8 31.6 - - + +
91B GLY* 2.7 43.9 + - - -
1092B FMT 2.8 36.7 + - - +
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Residues in contact with TRP 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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18B GLY* 3.8 22.4 - - - +
20B ARG* 1.3 84.5 - - - +
22B SER* 1.3 57.9 + - - +
24B GLN* 3.4 10.4 + - - +
25B ARG* 3.0 27.6 + - - +
89B ILE* 3.5 23.6 - - + +
1092B FMT 3.0 24.7 + - - -
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Residues in contact with SER 22 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18B GLY* 2.9 20.3 + - - -
19B PHE 4.0 0.7 - - - -
21B TRP* 1.3 74.5 - - - +
23B MET* 1.3 67.3 + - - +
25B ARG* 3.2 34.4 + - - +
26B GLU* 2.9 24.3 + - - +
61B TRP* 3.6 23.0 - - - -
66B PRO* 3.6 17.7 - - - +
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Residues in contact with MET 23 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B LEU* 4.8 4.0 - - + -
10B ILE* 3.8 27.1 - - + -
19B PHE* 2.8 27.8 + - + +
20B ARG* 3.9 4.9 - - - +
22B SER* 1.3 76.9 - - - +
24B GLN* 1.3 57.5 + - - +
26B GLU* 3.3 1.9 + - - +
27B ALA* 2.8 28.6 + - - +
36B VAL* 3.8 27.6 - - + -
46B ALA* 3.9 14.8 - - + -
48B LEU* 4.4 10.5 - - + -
58B LEU* 4.4 10.1 - - + -
61B TRP* 3.4 21.2 - - + -
62B ALA* 3.9 20.9 - - + -
87B PHE* 4.1 14.6 - - + -
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Residues in contact with GLN 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 3.0 16.5 + - - +
21B TRP* 3.6 11.1 + - - +
23B MET* 1.3 75.5 - - - +
25B ARG* 1.3 64.8 + - - +
27B ALA* 3.4 0.9 + - - +
28B ARG* 3.0 70.1 + - - +
87B PHE* 3.7 21.3 - - + -
88B ARG* 3.8 1.7 - - - +
89B ILE* 3.5 40.5 + - + +
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Residues in contact with ARG 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 TRP 3.0 14.9 + - - +
22B SER* 3.2 44.1 + - - +
24B GLN* 1.3 77.9 - - - +
26B GLU* 1.3 78.4 + - - +
28B ARG* 3.9 6.1 - - - +
29B LYS* 3.0 29.4 + - + +
61B TRP* 4.2 12.1 - - - +
66B PRO* 5.9 2.4 - - - +
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Residues in contact with GLU 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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56A GLU* 5.5 1.4 - - - +
22B SER 2.9 15.2 + - - +
23B MET 3.8 0.2 - - - +
25B ARG* 1.3 97.4 + - - +
27B ALA* 1.3 61.5 + - - +
29B LYS* 3.3 30.9 + - - +
30B LEU* 2.9 46.9 + - + +
58B LEU* 3.6 22.9 - - + -
61B TRP* 3.9 31.6 + - + +
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Residues in contact with ALA 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 MET 2.8 18.1 + - - +
24B GLN 3.7 1.8 - - - +
26B GLU* 1.3 76.9 - - - +
28B ARG* 1.3 56.9 + - - +
30B LEU* 3.2 1.3 + - - -
31B GLY 2.8 25.3 + - - -
32B VAL* 2.9 19.3 + - + +
58B LEU* 3.8 20.3 - - + +
87B PHE* 3.4 38.4 - - + -
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Residues in contact with ARG 28 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B GLN* 3.0 55.3 + - - +
25B ARG* 3.9 5.8 - - - +
27B ALA* 1.3 73.0 - - - +
29B LYS* 1.3 66.0 + - - +
30B LEU 3.5 0.2 + - - -
31B GLY* 3.5 9.3 + - - -
32B VAL 5.1 1.3 - - - -
87B PHE* 2.9 37.9 + - + +
88B ARG* 4.6 3.4 - - - +
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Residues in contact with LYS 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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53A GLU* 5.1 9.4 + - - -
25B ARG* 3.0 15.9 + - + +
26B GLU* 3.3 35.0 + - - +
28B ARG* 1.3 77.7 - - - +
30B LEU* 1.3 69.5 + - + +
31B GLY 3.6 0.3 + - - -
54B ARG* 4.7 3.1 + - - -
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Residues in contact with LEU 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 GLU* 2.9 38.0 + - + +
27B ALA 3.9 2.9 - - - +
29B LYS* 1.3 88.4 - - + +
31B GLY* 1.3 61.4 + - - +
32B VAL* 3.4 10.3 - - + -
54B ARG* 2.8 53.3 + - + +
57B ALA* 4.0 18.8 - - + -
58B LEU* 3.7 39.5 - - + +
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Residues in contact with GLY 31 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27B ALA 2.8 5.8 + - - -
28B ARG* 3.5 7.8 + - - -
29B LYS 3.4 3.2 + - - -
30B LEU* 1.3 79.1 - - - +
32B VAL* 1.3 62.2 + - - +
33B ASN* 4.0 12.6 + - - +
49B GLU 4.8 0.5 - - - +
50B GLY* 5.0 4.7 - - - -
51B ASP 5.4 0.9 + - - -
54B ARG* 4.9 4.6 - - - +
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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