Contacts of the helix formed by residues 24 - 46 (chain B) in PDB entry 1W2E
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 GLU 24 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A HIS* 2.8 41.3 + - - +
67A LEU* 3.9 24.6 - - + +
68A HIS* 3.7 18.5 + - - +
71A GLU* 5.8 0.7 - - - +
20B CYS* 4.4 1.1 - - + -
21B PRO* 2.7 36.8 + - + +
23B ASP* 1.3 86.7 - - - +
25B ARG* 1.3 65.8 + - - +
26B ALA 3.3 2.2 - - - -
27B ASN* 2.9 8.5 + - - +
28B LEU* 2.8 43.1 + - + +
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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
----------------------------------------------------------
7B LEU* 3.9 13.4 - - + +
20B CYS* 3.9 21.5 - - - -
22B ASP* 3.3 15.7 + - - +
24B GLU* 1.3 75.4 - - - +
26B ALA* 1.3 81.4 + - - +
28B LEU* 3.2 1.7 + - - +
29B GLU* 2.8 66.5 + - - +
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Residues in contact with ALA 26 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B ASP 5.1 0.2 + - - -
23B ASP 5.2 2.5 + - - +
24B GLU 3.3 0.8 - - - -
25B ARG* 1.3 98.0 - - - +
27B ASN* 1.3 60.8 + - - +
29B GLU* 3.5 9.5 + - - +
30B SER* 2.9 28.2 + - - -
33B ARG* 4.8 2.3 + - - -
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Residues in contact with ASN 27 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A THR* 4.7 2.2 - - + +
67A LEU* 3.4 41.5 - - + +
23B ASP 5.1 4.5 + - - +
24B GLU* 2.9 7.5 + - - +
26B ALA* 1.3 78.9 + - - +
28B LEU* 1.3 61.7 + - - +
30B SER* 3.3 10.5 + - - -
31B ALA* 3.0 26.2 + - - +
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Residues in contact with LEU 28 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A LEU* 3.9 31.8 - - + +
63A THR* 3.8 24.7 - - + -
64A HIS* 4.3 7.2 - - + +
67A LEU* 4.1 6.7 - - + -
7B LEU* 4.0 11.7 - - + -
9B VAL* 4.7 1.5 - - + +
18B ILE* 4.6 15.0 - - + -
20B CYS* 3.1 36.8 - - + -
24B GLU* 2.8 29.8 + - + +
25B ARG 3.7 3.6 - - - +
27B ASN* 1.3 73.5 - - - +
29B GLU* 1.3 60.9 + - - +
31B ALA* 3.1 5.1 + - - +
32B ALA* 2.9 27.9 + - - +
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Residues in contact with GLU 29 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B LEU* 3.8 22.8 - - + +
9B VAL* 4.4 13.9 - - + -
25B ARG* 2.8 59.9 + - - +
26B ALA* 3.7 8.2 - - - +
28B LEU* 1.3 76.4 - - - +
30B SER* 1.3 64.1 - - - +
32B ALA* 3.2 3.9 + - - +
33B ARG* 2.9 38.1 + - - +
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Residues in contact with SER 30 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B ALA 2.9 19.0 + - - -
27B ASN* 3.4 14.1 - - - -
29B GLU* 1.3 77.9 - - - +
31B ALA* 1.3 61.1 + - - +
33B ARG* 3.4 28.3 + - - +
34B TYR* 3.1 20.4 + - - +
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Residues in contact with ALA 31 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A LEU* 4.6 7.4 - - + -
63A THR* 3.9 27.1 - - + +
27B ASN 3.0 13.0 + - - +
28B LEU* 3.2 10.5 - - - +
30B SER* 1.3 73.8 - - - +
32B ALA* 1.3 64.7 - - - +
34B TYR* 2.9 7.6 + - - +
35B LEU* 2.9 25.4 + - + +
62B ILE* 4.0 20.0 - - + +
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Residues in contact with ALA 32 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A LEU* 4.5 2.8 - - + +
9B VAL* 3.8 24.5 - - + -
10B GLN 4.7 3.6 - - - +
11B ILE* 3.7 32.7 - - + +
28B LEU 2.9 12.1 + - - +
29B GLU* 3.2 8.5 + - - +
31B ALA* 1.3 74.4 - - - +
33B ARG* 1.3 64.3 + - - +
35B LEU* 3.0 6.8 + - - +
36B ASP* 2.9 26.7 + - - +
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Residues in contact with ARG 33 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10B GLN 5.8 0.7 - - - -
26B ALA 4.8 1.4 + - - -
29B GLU* 2.9 21.9 + - - +
30B SER* 3.4 47.9 + - - +
32B ALA* 1.3 76.3 - - - +
34B TYR* 1.3 61.9 + - - +
36B ASP* 3.7 5.7 + - - +
37B GLY* 3.1 19.1 + - - -
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Residues in contact with TYR 34 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30B SER 3.1 12.8 + - - +
31B ALA* 2.9 10.6 + - - +
33B ARG* 1.3 73.7 - - - +
35B LEU* 1.3 70.8 + - + +
37B GLY* 3.2 2.5 + - - -
38B LYS* 2.9 46.7 + - + +
58B ALA 4.6 1.6 - - - -
61B ASN* 3.3 28.9 + - + -
62B ILE* 3.5 47.1 - - + -
65B ASP* 3.9 21.1 + - - -
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Residues in contact with LEU 35 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A VAL* 4.6 10.3 - - + +
59A ALA* 3.9 23.1 - - + -
60A LEU* 4.3 21.1 - - + -
11B ILE* 3.9 20.0 - - + -
31B ALA* 2.9 16.2 + - + +
32B ALA 3.3 8.3 - - - +
34B TYR* 1.3 79.7 - - + +
36B ASP* 1.3 58.4 + - - +
38B LYS* 3.1 4.0 + - - +
39B MSE 2.8 40.3 + - - +
55B ALA 5.6 0.2 - - - +
58B ALA* 3.9 33.4 - - + +
59B ALA* 4.3 2.7 - - + +
62B ILE* 4.2 21.5 - - + -
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Residues in contact with ASP 36 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10B GLN* 4.2 8.1 - - - +
11B ILE* 3.6 14.2 - - - +
12B LEU* 2.5 30.3 + - - +
13B ASP 4.4 0.7 + - - -
32B ALA 2.9 18.3 + - - +
33B ARG* 3.9 5.8 - - - +
35B LEU* 1.3 73.0 - - - +
37B GLY* 1.3 63.8 + - - +
39B MSE 3.4 4.4 + - - +
40B ARG* 2.8 62.9 + - - +
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Residues in contact with GLY 37 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B ARG 3.1 12.7 + - - -
34B TYR* 3.7 2.7 - - - -
36B ASP* 1.3 82.4 + - - +
38B LYS* 1.3 62.5 + - - +
40B ARG* 3.3 8.6 + - - +
41B GLU* 3.1 24.6 + - - +
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Residues in contact with LYS 38 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34B TYR* 2.9 40.2 + - + +
35B LEU* 3.6 3.6 - - - +
37B GLY* 1.3 75.5 - - - +
39B MSE 1.3 57.6 + - - +
41B GLU* 3.3 35.8 + - - +
42B ILE* 3.0 48.6 + - + +
58B ALA* 4.0 16.4 - - + -
61B ASN* 3.7 32.8 - - + +
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Residues in contact with MSE 39 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A ASP* 5.1 5.2 - - + +
56A VAL* 3.7 18.6 - - + -
11B ILE* 3.7 29.2 - - + +
12B LEU* 4.0 28.5 - - + -
16B TYR* 5.4 2.5 - - - +
35B LEU* 2.8 21.0 + - - +
36B ASP 3.8 4.0 - - - +
38B LYS* 1.3 73.0 - - - +
40B ARG* 1.3 59.9 + - - +
42B ILE* 3.4 0.8 + - - -
43B ARG* 2.8 32.4 + - - +
51B ALA 4.9 2.0 - - - +
54B VAL* 3.6 19.5 - - + +
55B ALA* 3.6 34.5 - - + +
58B ALA* 3.3 22.9 - - + -
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Residues in contact with ARG 40 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B LEU* 3.4 26.2 - - + +
13B ASP* 3.3 20.0 + - - +
36B ASP* 2.8 60.6 + - - +
37B GLY* 3.7 7.6 - - - +
39B MSE 1.3 76.1 - - - +
41B GLU* 1.3 58.2 + - - +
43B ARG* 3.8 25.3 + - - +
44B SER* 2.9 32.6 + - - -
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Residues in contact with GLU 41 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B GLY 3.1 12.7 + - - +
38B LYS* 3.3 43.8 + - - +
39B MSE 3.2 0.2 - - - -
40B ARG* 1.3 78.0 - - - +
42B ILE* 1.3 61.6 + - + +
44B SER* 3.3 7.6 + - - -
45B SER* 3.0 27.1 + - - -
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Residues in contact with ILE 42 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B LYS* 3.0 44.8 + - + +
39B MSE 3.9 2.9 - - - +
41B GLU* 1.3 74.6 - - + +
43B ARG* 1.3 68.1 + - - +
45B SER* 2.8 27.3 + - - +
46B GLY* 3.3 3.8 + - - -
47B LYS 4.3 1.2 + - - -
48B VAL* 3.9 34.3 + - + +
54B VAL* 4.2 16.6 - - + +
57B MSE 3.9 13.9 - - + +
58B ALA* 3.9 23.1 - - + +
61B ASN* 5.0 3.1 - - - +
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Residues in contact with ARG 43 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B LEU* 3.7 41.7 - - - +
13B ASP* 5.1 4.2 + - - -
39B MSE 2.8 22.0 + - - +
40B ARG* 3.8 27.5 + - - +
42B ILE* 1.3 74.7 - - - +
44B SER* 1.3 63.8 + - - +
46B GLY* 3.1 14.9 + - - -
48B VAL 5.3 2.6 - - - +
54B VAL* 4.3 18.6 - - + +
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Residues in contact with SER 44 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40B ARG 2.9 20.0 + - - -
41B GLU* 3.5 6.6 + - - -
43B ARG* 1.3 79.9 - - - +
45B SER* 1.3 61.6 + - - +
46B GLY* 3.4 0.7 + - - -
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Residues in contact with SER 45 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41B GLU* 3.0 14.3 + - - -
42B ILE* 2.8 21.0 + - - +
44B SER* 1.3 77.8 - - - +
46B GLY* 1.3 58.0 + - - +
47B LYS* 2.9 39.6 + - - +
48B VAL 4.5 0.5 + - - -
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Residues in contact with GLY 46 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42B ILE 3.3 1.8 + - - -
43B ARG 3.1 15.4 + - - -
44B SER 3.2 1.9 - - - -
45B SER* 1.3 76.5 + - - +
47B LYS* 1.3 61.9 + - - +
48B VAL 3.1 8.6 + - - -
49B ILE* 4.0 17.0 - - - +
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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
------------------------------------------------------------
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) + - + + + + + -
------------------------------------------------------------
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