Contacts of the helix formed by residues 22 - 45 (chain B) in PDB entry 2QNU
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 PRO 22 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20B GLY 4.4 3.6 - - - +
21B LEU* 1.3 89.3 - - + +
23B ASN* 1.3 64.2 + - - +
24B THR* 3.1 25.4 - - + +
25B PHE* 3.1 5.3 + - + +
26B VAL* 3.1 18.4 + - - +
70B GLU* 5.2 1.3 - - - +
94B LEU* 3.8 32.8 - - + -
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Residues in contact with ASN 23 (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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22B PRO* 1.3 68.6 - - - +
24B THR* 1.3 65.6 + - - +
25B PHE 3.0 2.5 - - - -
26B VAL* 3.6 11.8 - - - +
27B GLU* 2.9 75.2 + - - +
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Residues in contact with THR 24 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B PRO* 3.5 22.3 - - + +
23B ASN* 1.3 77.5 - - - +
25B PHE* 1.3 61.5 + - - +
28B PRO* 3.0 23.5 - - - +
68B GLY* 3.6 22.3 + - - -
69B GLY 5.5 1.1 - - - -
70B GLU* 4.2 11.9 + - - +
94B LEU* 4.6 0.9 - - - +
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Residues in contact with PHE 25 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B TYR* 5.1 1.3 - - + -
21B LEU* 3.8 33.9 - - + -
22B PRO* 3.1 8.9 + - + +
23B ASN 3.0 0.2 - - - -
24B THR* 1.3 87.3 + - - +
26B VAL* 1.3 67.7 + - + +
28B PRO* 3.3 5.1 - - - +
29B TRP* 2.9 82.8 + + + +
60B PHE* 5.5 0.2 - + - -
67B LEU* 4.0 20.4 - - + -
68B GLY* 4.9 3.8 - - - +
72B VAL* 3.7 27.6 - - + -
90B THR* 5.1 1.3 - - + -
92B ALA* 4.2 14.4 - - + -
94B LEU* 3.9 22.4 - - + -
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Residues in contact with VAL 26 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B TYR* 3.7 37.7 - - + +
18B SER* 3.9 15.0 - - - +
21B LEU* 3.9 26.5 - - + +
22B PRO 3.1 18.2 + - - +
23B ASN* 3.2 11.2 + - - +
25B PHE* 1.3 81.4 - - + +
27B GLU* 1.3 69.9 + - - +
29B TRP* 3.1 3.0 + - - -
30B ASP* 2.7 28.9 + - + +
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Residues in contact with GLU 27 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B ASN* 2.9 48.1 + - - +
26B VAL* 1.3 74.2 - - - +
28B PRO* 1.4 69.2 - - + +
30B ASP* 3.6 5.4 + - - +
31B ALA* 3.1 21.7 + - - +
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Residues in contact with PRO 28 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B ASN 3.6 0.2 - - - +
24B THR 3.0 29.8 - - - +
25B PHE 3.3 10.3 - - - +
27B GLU* 1.4 93.8 - - + +
29B TRP* 1.3 63.2 + - - +
31B ALA* 3.9 6.1 - - + +
32B TRP* 2.9 26.5 + - - +
66B LEU 5.2 0.9 - - - +
67B LEU* 3.8 35.0 - - + +
201B LEU* 6.2 0.4 - - + -
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Residues in contact with TRP 29 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B TYR* 3.9 17.4 - + - -
25B PHE* 2.9 49.8 + + + +
26B VAL* 3.7 2.2 - - - +
28B PRO* 1.3 77.8 - - - +
30B ASP* 1.3 59.6 + - - +
32B TRP* 3.2 37.6 + + - +
33B LEU* 2.9 51.5 + - + +
60B PHE* 4.1 20.0 - + - -
62B ILE* 3.9 22.2 - - + -
67B LEU* 3.9 21.3 - - + +
76B VAL* 4.4 5.8 - - + -
90B THR* 3.1 43.5 + - + +
183B TRP* 4.1 8.5 - + - -
201B LEU* 5.7 1.1 - - + -
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Residues in contact with ASP 30 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B TYR* 2.6 39.7 + - + +
16B PHE* 4.1 7.4 - - - -
26B VAL* 2.7 22.4 + - + +
27B GLU* 3.7 5.2 - - - +
29B TRP* 1.3 75.1 - - - +
31B ALA* 1.3 61.1 + - - +
33B LEU* 3.2 5.0 + - - +
34B ALA* 2.8 34.2 + - - +
87B PHE* 3.8 12.9 - - - -
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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
----------------------------------------------------------
27B GLU 3.1 18.7 + - - +
28B PRO* 3.9 7.2 - - + +
30B ASP* 1.3 79.0 - - - +
32B TRP* 1.3 57.0 + - - +
34B ALA* 3.9 5.3 - - - +
35B SER* 2.6 35.5 + - - +
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Residues in contact with TRP 32 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28B PRO 2.9 18.1 + - - +
29B TRP* 3.5 35.7 - + - +
31B ALA* 1.3 80.3 - - - +
33B LEU* 1.3 96.0 + - + +
35B SER* 3.8 7.0 - - - -
36B GLY* 3.2 18.2 + - - -
67B LEU* 5.0 0.7 - - + -
76B VAL* 6.1 0.7 - - + -
183B TRP* 3.5 20.0 - + - -
201B LEU* 3.9 32.7 - - + +
202B PRO* 2.8 55.6 + - + -
203B PRO 5.1 1.0 - - - -
204B ALA* 5.5 4.6 - - - +
207B PHE* 4.1 20.1 - + - -
210B PHE* 4.1 9.9 - + - -
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Residues in contact with LEU 33 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B TYR* 5.2 1.1 - - + +
29B TRP* 2.9 52.0 + - + +
30B ASP 3.2 0.9 + - - +
32B TRP* 1.3 98.4 - - + +
34B ALA* 1.3 59.6 + - - +
36B GLY* 3.2 2.8 + - - -
37B MSE 2.8 35.7 + - + +
76B VAL* 4.9 4.9 - - + -
87B PHE* 3.7 33.9 - - + -
88B PRO* 4.1 22.9 - - + +
90B THR* 4.4 5.6 - - - +
207B PHE* 4.0 17.8 - - + -
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Residues in contact with ALA 34 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30B ASP* 2.8 23.6 + - - +
31B ALA* 3.9 6.1 - - - +
33B LEU* 1.3 78.4 - - - +
35B SER* 1.3 56.6 + - - +
37B MSE 3.4 8.5 + - - +
38B ARG* 3.1 30.1 + - - +
87B PHE* 4.3 11.4 - - + -
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Residues in contact with SER 35 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31B ALA* 2.6 25.3 + - - +
32B TRP* 3.8 7.5 - - - -
34B ALA* 1.3 74.6 - - - +
36B GLY* 1.3 58.4 + - - +
38B ARG* 3.7 4.8 + - - +
39B ALA* 2.9 30.3 + - - +
204B ALA* 3.7 19.2 - - - +
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Residues in contact with GLY 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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32B TRP* 3.2 6.8 + - - -
33B LEU 3.2 5.9 + - - -
35B SER* 1.3 79.3 - - - +
37B MSE 1.3 58.2 + - - +
40B SER* 2.9 30.1 + - - -
204B ALA* 4.0 9.6 - - - +
207B PHE* 3.2 38.9 - - - +
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Residues in contact with MSE 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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33B LEU 2.8 28.2 + - - +
34B ALA* 3.6 8.3 - - - +
35B SER 3.3 0.2 - - - -
36B GLY* 1.3 73.9 - - - +
38B ARG* 1.3 58.8 + - - +
40B SER* 2.6 21.6 + - - -
41B GLN* 2.8 32.7 + - - +
48B TRP* 3.6 29.8 - - + -
52B TYR* 3.8 23.3 - - + -
86B TYR 3.5 30.7 - - - +
87B PHE* 4.1 7.4 - - + -
88B PRO* 3.8 19.7 - - + -
207B PHE* 4.0 16.8 - - + -
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Residues in contact with ARG 38 (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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34B ALA 3.1 15.0 + - - +
35B SER* 3.9 5.4 - - - +
37B MSE 1.3 79.0 - - - +
39B ALA* 1.3 61.6 + - - +
41B GLN* 2.8 46.3 + - - +
42B ASP* 2.6 57.1 + - - +
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Residues in contact with ALA 39 (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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35B SER 2.9 19.2 + - - +
38B ARG* 1.3 76.5 - - - +
40B SER* 1.3 63.1 + - - +
42B ASP* 3.2 10.0 + - - +
43B GLU* 2.9 32.7 + - - +
204B ALA* 3.5 30.1 - - + +
205B PRO* 4.1 9.6 - - + -
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Residues in contact with SER 40 (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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36B GLY 2.9 19.5 + - - -
37B MSE 2.6 24.8 + - - -
39B ALA* 1.3 71.5 - - - +
41B GLN* 1.3 55.2 + - - +
43B GLU* 3.3 10.7 + - - +
44B LEU* 2.9 37.3 + - - +
48B TRP* 3.0 20.1 + - - -
204B ALA 4.8 1.2 + - - -
207B PHE* 3.8 7.7 - - - -
208B GLY* 3.9 22.7 - - - +
211B LEU* 3.9 9.6 - - - +
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Residues in contact with GLN 41 (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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37B MSE 2.8 37.0 + - - +
38B ARG* 2.8 46.1 + - - +
40B SER* 1.3 73.1 + - - +
42B ASP* 1.3 56.3 + - - +
45B GLY* 2.9 29.6 + - - +
48B TRP* 3.3 57.4 - - + -
86B TYR* 5.5 1.2 - - - +
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Residues in contact with ASP 42 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B ARG* 2.6 55.5 + - - +
39B ALA* 3.2 9.2 + - - +
41B GLN* 1.3 75.8 - - - +
43B GLU* 1.3 62.9 + - + +
45B GLY* 4.1 4.9 + - - -
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Residues in contact with GLU 43 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39B ALA* 2.9 25.9 + - - +
40B SER* 3.7 8.3 - - - +
42B ASP* 1.3 80.6 - - + +
44B LEU* 1.3 66.0 + - + +
45B GLY 3.6 0.2 - - - -
205B PRO* 3.3 43.6 - - - +
208B GLY* 4.8 7.3 + - - -
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Residues in contact with LEU 44 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40B SER* 2.9 21.1 + - - +
43B GLU* 1.3 83.7 - - + +
45B GLY* 1.3 65.8 + - - +
46B ALA 3.4 0.5 + - - -
47B ALA* 3.1 27.4 + - + +
48B TRP* 3.7 35.0 - - + +
51B ALA* 4.2 8.3 - - + -
208B GLY* 5.0 5.8 - - - -
211B LEU* 4.2 10.5 - - + -
212B THR* 4.1 30.7 - - + -
214B GLU* 5.0 6.7 - - - +
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Residues in contact with GLY 45 (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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41B GLN 2.9 17.9 + - - +
42B ASP 4.1 4.4 + - - -
43B GLU 3.6 1.2 - - - -
44B LEU* 1.3 74.2 - - - +
46B ALA* 1.3 57.1 + - - -
48B TRP* 2.9 27.2 + - - +
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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
------------------------------------------------------------
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) + - + + + + + -
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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