Contacts of the helix formed by residues 32 - 49 (chain X) in PDB entry 2QW0
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 HIS 32 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8X LEU* 4.9 1.8 + - - -
11X ALA* 4.0 8.2 - - + +
12X ALA* 4.0 29.2 + - - +
15X ALA* 3.4 23.6 - - + +
16X PRO 3.5 0.4 + - - +
18X HIS* 2.9 23.8 + + + -
19X CYS 4.2 1.1 - - - -
20X ALA* 3.6 19.5 - - + +
31X THR* 1.3 71.6 - - - +
33X ALA* 1.3 57.0 + - - +
35X LEU* 3.3 4.2 + - - +
36X ARG* 3.0 32.4 + - - +
219X LEU* 3.2 43.5 - - + +
222X ASP* 3.9 8.5 - - - -
223X GLY 2.9 22.8 + - - -
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Residues in contact with ALA 33 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12X ALA* 5.2 2.7 - - - -
16X PRO* 2.7 40.6 + - + +
17X ASP* 4.6 5.4 - - - +
31X THR* 3.8 2.5 - - - +
32X HIS* 1.3 69.1 - - - +
34X GLU* 1.3 67.5 + - + +
36X ARG* 3.4 8.5 + - - +
37X ALA* 3.1 23.2 + - - +
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Residues in contact with GLU 34 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29X ARG 4.0 3.6 - - - +
30X LEU* 3.5 17.8 - - + +
31X THR* 2.9 45.5 + - - +
33X ALA* 1.3 77.5 - - + +
35X LEU* 1.3 63.4 + - - +
37X ALA* 3.3 3.9 + - - -
38X ARG* 3.1 52.5 + - - +
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Residues in contact with LEU 35 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20X ALA* 3.9 18.6 - - + -
21X LEU* 3.9 20.6 - - + -
30X LEU* 4.6 8.0 - - + +
31X THR 2.8 17.6 + - - +
32X HIS* 3.7 6.3 - - - +
34X GLU* 1.3 74.3 - - - +
36X ARG* 1.3 68.6 + - - +
38X ARG* 3.5 5.8 + - - +
39X VAL* 3.0 32.0 + - + +
68X VAL* 4.8 2.2 - - + -
69X ILE* 3.8 27.8 - - + -
72X LEU* 4.7 9.9 - - + -
219X LEU* 3.7 30.5 - - + -
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Residues in contact with ARG 36 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5X ASN* 3.0 31.3 + - - +
8X LEU* 3.3 45.1 + - - +
9X ARG* 4.4 16.7 - - - +
12X ALA* 3.5 30.5 - - + -
32X HIS 3.0 10.0 + - - +
33X ALA* 3.6 10.1 - - - +
35X LEU* 1.3 77.8 - - - +
37X ALA* 1.3 51.5 + - - +
39X VAL* 2.9 37.8 + - - +
40X GLU* 2.8 58.0 + - + +
72X LEU* 4.5 4.9 + - - +
76X ARG* 4.5 1.0 - - - +
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Residues in contact with ALA 37 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33X ALA 3.1 13.8 + - - +
34X GLU* 3.3 10.5 + - - +
36X ARG* 1.3 74.4 - - - +
38X ARG* 1.3 67.5 + - - +
40X GLU* 3.5 8.3 + - - +
41X ALA* 3.0 27.4 + - - +
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Residues in contact with ARG 38 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30X LEU* 3.8 38.2 - - - +
34X GLU* 3.1 40.9 + - - +
35X LEU* 4.0 4.7 - - - +
36X ARG 3.2 0.6 - - - -
37X ALA* 1.3 82.2 - - - +
39X VAL* 1.3 67.0 + - - +
41X ALA 4.4 0.2 - - - +
42X VAL* 2.9 30.1 + - - +
69X ILE* 4.1 21.3 - - + -
136X GLY 2.9 26.8 + - - +
137X GLU* 2.9 21.1 + - - -
138X PRO* 3.8 23.3 - - + -
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Residues in contact with VAL 39 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35X LEU* 3.0 33.4 + - + +
36X ARG* 2.9 30.2 + - - +
38X ARG* 1.3 74.5 - - - +
40X GLU* 1.3 57.4 + - - +
43X ALA* 3.0 30.0 + - - +
69X ILE* 4.2 9.8 - - - +
72X LEU* 3.5 49.6 - - + +
73X ALA* 3.8 7.8 - - - +
76X ARG* 3.6 18.2 - - + -
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Residues in contact with GLU 40 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36X ARG* 2.8 43.9 + - + +
37X ALA* 3.8 7.4 - - - +
39X VAL* 1.3 73.7 - - - +
41X ALA* 1.3 56.5 + - - +
43X ALA* 3.3 5.6 - - - +
44X ALA* 2.9 29.6 + - - +
76X ARG* 3.1 45.3 + - - -
144X PRO* 5.7 7.5 - - + +
145X ILE* 5.2 5.0 + - - +
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Residues in contact with ALA 41 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37X ALA 3.0 17.9 + - - +
38X ARG 3.3 2.2 + - - +
40X GLU* 1.3 73.9 - - - +
42X VAL* 1.3 65.5 + - - +
44X ALA* 3.5 6.7 + - - +
45X ARG* 3.1 23.4 + - - +
138X PRO* 4.5 12.1 - - + -
139X TYR 4.8 2.7 - - - +
140X SER* 3.4 29.5 - - - +
141X TYR 5.1 1.0 + - - +
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Residues in contact with VAL 42 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38X ARG 2.9 20.1 + - - +
41X ALA* 1.3 75.1 - - - +
43X ALA* 1.3 62.1 + - - +
45X ARG* 3.3 6.9 + - - +
46X LEU* 3.1 26.7 + - + +
69X ILE* 3.9 15.3 - - + -
70X ALA* 4.7 6.1 - - - -
73X ALA* 3.6 22.2 - - + -
132X LEU* 3.9 42.2 - - + +
133X VAL* 4.3 3.6 - - + -
138X PRO* 3.6 24.9 - - + -
139X TYR 5.5 0.9 - - - +
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Residues in contact with ALA 43 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39X VAL 3.0 21.5 + - - +
40X GLU* 3.3 6.5 - - - +
42X VAL* 1.3 74.7 - - - +
44X ALA* 1.3 63.9 + - - +
45X ARG 3.0 0.5 + - - -
46X LEU* 3.1 5.3 + - - -
47X HIS* 3.0 19.1 + - - +
73X ALA* 3.8 23.8 - - - +
76X ARG* 4.0 13.9 - - + +
77X LEU* 3.4 11.1 - - - +
145X ILE* 3.7 18.6 - - + -
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Residues in contact with ALA 44 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40X GLU 2.9 18.5 + - - +
41X ALA* 3.9 7.0 - - - +
43X ALA* 1.3 74.0 - - - +
45X ARG* 1.3 52.9 + - - +
47X HIS* 3.3 1.9 + - - +
48X ALA* 2.7 35.0 + - - +
141X TYR 4.1 8.2 - - - +
142X GLY* 4.6 2.5 - - - +
143X PRO 3.3 28.6 - - - +
144X PRO* 4.5 5.4 - - + -
145X ILE* 3.7 19.9 - - + +
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Residues in contact with ARG 45 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41X ALA 3.1 17.7 + - - +
42X VAL* 3.6 7.4 - - - +
43X ALA 3.0 0.6 + - - -
44X ALA* 1.3 76.5 - - - +
46X LEU* 1.3 63.4 + - - +
48X ALA* 3.4 3.9 + - - +
49X ASP* 3.2 37.0 + - - -
131X ASP* 2.5 40.8 + - - +
132X LEU* 3.4 28.0 - - - +
139X TYR* 3.4 34.6 - - - +
141X TYR* 3.2 58.2 + - + +
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Residues in contact with LEU 46 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42X VAL* 3.1 30.9 + - + +
43X ALA* 3.6 4.9 - - - +
45X ARG* 1.3 74.7 - - - +
47X HIS* 1.3 59.6 + - - +
49X ASP* 3.1 23.2 + - - +
50X GLY 3.5 0.3 + - - -
51X LEU* 3.3 30.9 + - + +
70X ALA 5.1 0.2 - - - +
73X ALA* 4.5 0.9 - - + -
74X LEU* 3.8 39.0 - - + +
77X LEU* 3.6 14.4 - - + -
106X VAL* 5.5 0.7 - - + -
125X ARG* 5.1 2.4 + - - +
127X ILE* 4.4 18.6 - - + -
132X LEU* 3.8 34.8 - - + -
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Residues in contact with HIS 47 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43X ALA 3.0 13.2 + - - +
44X ALA 3.6 7.0 - - - +
46X LEU* 1.3 77.3 - - - +
48X ALA* 1.3 64.0 + - - +
49X ASP 3.1 0.9 - - - -
50X GLY 3.2 5.5 + - - -
51X LEU 3.6 13.2 - - - -
52X ARG* 2.9 53.2 + - - -
53X PRO* 5.3 3.9 - - + +
77X LEU* 3.7 15.5 - - + -
145X ILE* 3.9 35.1 - - + +
146X GLU* 5.0 9.1 + - - -
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Residues in contact with ALA 48 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44X ALA 2.7 21.1 + - - +
45X ARG 3.7 6.7 - - - +
46X LEU 3.3 0.2 - - - -
47X HIS* 1.3 76.0 + - - +
49X ASP* 1.3 61.3 + - - +
50X GLY 3.4 0.6 + - - -
52X ARG* 5.8 0.2 - - - -
141X TYR* 4.2 26.2 - - + +
142X GLY* 4.7 8.7 - - - -
143X PRO* 6.0 0.9 - - + -
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Residues in contact with ASP 49 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45X ARG* 3.2 23.4 + - - +
46X LEU* 3.1 15.6 + - - +
47X HIS 3.1 1.2 - - - -
48X ALA* 1.3 79.4 - - - +
50X GLY* 1.3 55.6 + - - +
51X LEU 3.6 1.3 - - - -
125X ARG* 2.9 38.6 + - - +
132X LEU* 5.6 1.4 - - - +
141X TYR* 3.0 30.9 + - - -
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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