Contacts of the helix formed by residues 31 - 45 (chain E) in PDB entry 1W4R
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 31 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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29E PHE* 3.4 3.8 - - - +
30E SER* 1.3 78.9 - - - +
32E LYS* 1.3 64.4 + - - +
33E SER 3.3 2.7 - - - -
34E THR* 3.1 9.9 + - - -
35E GLU* 3.0 19.2 + - - +
149E LEU* 4.0 1.3 - - - -
300E TTP 3.2 12.9 + - - -
38F ARG* 3.3 22.2 - - - -
42F ARG* 4.9 1.1 - - - +
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Residues in contact with LYS 32 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24E ILE* 3.9 7.3 - - + +
25E LEU 3.7 10.5 - - - +
26E GLY* 3.5 21.3 - - - +
27E PRO 3.0 17.6 + - - -
28E MET* 4.1 0.6 - - - +
30E SER* 3.3 11.8 - - - +
31E GLY* 1.3 75.5 - - - +
33E SER* 1.3 54.9 + - - +
35E GLU* 3.3 2.9 + - - +
36E LEU* 2.9 27.9 + - - +
122E ALA* 3.8 17.8 - - + +
123E ALA 3.4 33.2 - - - +
124E LEU* 3.6 3.0 - - - +
149E LEU* 3.9 11.2 - - + -
300E TTP 2.8 68.6 + - - +
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Residues in contact with SER 33 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32E LYS* 1.3 70.9 - - - +
34E THR* 1.3 63.8 + - - +
36E LEU* 3.5 7.5 - - - +
37E MET* 3.0 34.4 + - - +
97E ASP* 3.4 30.5 - - - -
122E ALA* 4.6 0.2 - - - -
300E TTP 2.6 35.8 + - - -
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Residues in contact with THR 34 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31E GLY* 3.1 15.5 + - - -
33E SER* 1.3 82.2 + - - +
35E GLU* 1.3 56.1 + - - +
37E MET* 3.2 6.1 + - - +
38E ARG* 2.8 27.9 + - - +
300E TTP 5.2 0.2 + - - -
34F THR* 3.8 21.2 - - + +
38F ARG* 3.7 29.1 - - + -
41F ARG* 3.8 27.2 + - - +
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Residues in contact with GLU 35 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24E ILE* 3.9 14.1 - - + -
31E GLY 3.0 12.7 + - - +
32E LYS 3.7 6.7 - - - +
34E THR* 1.3 74.2 - - - +
36E LEU* 1.3 65.0 + - - +
38E ARG* 2.8 41.3 + - - +
39E ARG* 2.8 59.2 + - - +
149E LEU* 4.2 18.2 - - + -
35F GLU* 3.7 13.3 - - - +
38F ARG* 4.2 6.9 - - - +
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Residues in contact with LEU 36 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24E ILE* 3.7 10.8 - - + +
32E LYS 2.9 14.0 + - - +
33E SER* 3.5 11.4 - - - +
35E GLU* 1.3 75.2 - - - +
37E MET* 1.3 63.4 + - + +
39E ARG* 3.1 4.2 + - - +
40E VAL* 2.9 37.2 + - + +
52E VAL* 4.5 9.9 - - + -
95E GLY* 3.9 10.8 - - - -
96E ILE 3.8 29.2 - - - +
97E ASP* 3.9 18.6 - - + +
120E ILE* 3.4 44.4 - - + +
121E VAL 4.5 0.4 - - - +
122E ALA* 4.3 7.2 - - + +
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Residues in contact with MET 37 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33E SER* 3.0 19.3 + - - +
34E THR* 3.8 5.2 - - - +
36E LEU* 1.3 82.1 - - + +
38E ARG* 1.3 66.8 + - - +
40E VAL* 4.4 8.3 - - + -
41E ARG* 2.9 72.4 + - + +
44E GLN* 6.0 2.2 - - - +
52E VAL* 3.8 38.6 - - + -
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Residues in contact with ARG 38 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34E THR 2.8 14.3 + - - +
35E GLU* 2.8 47.2 + - - +
37E MET* 1.3 76.8 - - - +
39E ARG* 1.3 71.5 + - - +
41E ARG* 3.4 7.3 + - - +
42E ARG* 3.2 42.1 + - - +
30F SER 2.8 28.4 + - - +
31F GLY* 3.3 36.1 - - - +
34F THR* 3.7 14.4 - - + -
35F GLU* 4.2 16.5 + - - +
149F LEU* 3.9 25.9 - - - +
150F THR 4.4 1.2 + - - +
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Residues in contact with ARG 39 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22E GLN* 2.9 43.5 + - - +
23E VAL 4.9 1.8 + - - -
24E ILE* 3.7 18.3 - - - +
35E GLU* 2.8 39.3 + - - +
36E LEU 3.1 7.4 + - - +
38E ARG* 1.3 85.3 - - - +
40E VAL* 1.3 63.3 + - - +
42E ARG* 3.3 26.3 + - - +
43E PHE* 3.2 21.7 - - - -
120E ILE* 3.9 20.2 - - + -
145E SER* 4.1 9.2 + - - -
147E VAL* 3.7 35.0 - - - +
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Residues in contact with VAL 40 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36E LEU* 2.9 36.4 + - + +
37E MET* 3.9 14.6 - - + +
39E ARG* 1.3 75.0 - - - +
41E ARG* 1.3 59.8 + - + +
43E PHE* 3.0 13.1 + - - +
44E GLN* 2.9 28.5 + - + +
50E CYS* 3.8 28.4 - - + -
51E LEU 5.5 0.2 - - - +
52E VAL* 4.2 19.3 - - + -
93E VAL* 4.6 7.0 - - + -
95E GLY* 4.3 15.5 - - - +
120E ILE* 4.4 10.3 - - + -
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Residues in contact with ARG 41 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37E MET* 2.9 70.3 + - + +
38E ARG* 3.9 8.4 - - - +
40E VAL* 1.3 77.6 - - + +
42E ARG* 1.3 61.9 + - - +
44E GLN* 3.7 22.3 - - - +
45E ILE* 3.0 27.7 + - - +
34F THR* 4.0 23.4 + - - +
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Residues in contact with ARG 42 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22E GLN* 5.7 2.2 + - - +
38E ARG* 3.2 42.9 + - - +
39E ARG* 3.4 29.5 + - - +
40E VAL 3.2 0.4 - - - -
41E ARG* 1.3 77.4 - - - +
43E PHE* 1.3 80.2 + - - +
45E ILE* 3.4 19.7 - - - +
46E ALA* 3.8 3.1 + - - +
29F PHE 3.8 18.8 - - - +
30F SER 3.9 6.3 - - - +
31F GLY* 4.9 0.9 - - - +
150F THR* 2.9 37.2 + - - -
151F ALA* 3.9 13.7 + - - +
152F VAL* 3.7 28.3 + - + +
159F GLU* 4.7 8.7 + - - +
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Residues in contact with PHE 43 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20E GLN* 5.0 4.7 - - - -
22E GLN* 4.8 9.4 - - - -
39E ARG 3.2 25.1 - - - -
40E VAL 3.0 5.9 + - - +
42E ARG* 1.3 93.3 - - - +
44E GLN* 1.3 67.3 + - - +
46E ALA* 3.0 11.5 + - - -
48E TYR* 3.1 50.5 + + + -
50E CYS* 4.3 2.0 - - - -
93E VAL* 3.8 35.2 - - + -
118E THR* 4.2 20.9 - - + -
120E ILE* 4.1 16.8 - - + -
152F VAL* 3.9 17.7 - - + -
157F PHE 5.9 1.6 - - - -
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Residues in contact with GLN 44 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37E MET* 6.0 2.1 - - - +
40E VAL* 2.9 19.6 + - - +
41E ARG* 3.2 24.5 + - - +
43E PHE* 1.3 75.7 - - - +
45E ILE* 1.3 56.7 + - - +
47E GLN* 2.9 21.3 + - - +
48E TYR 3.8 13.5 + - - +
50E CYS* 4.0 24.0 + - - +
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Residues in contact with ILE 45 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41E ARG 3.0 14.5 + - - +
42E ARG* 3.4 18.6 - - - +
44E GLN* 1.3 76.2 - - - +
46E ALA* 1.3 59.0 + - + +
47E GLN* 3.2 8.7 + - - +
29F PHE* 3.4 44.2 - - + +
152F VAL 6.1 0.7 - - - +
154F MET* 3.9 24.7 - - + +
178F ALA* 4.7 10.2 - - + +
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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