Contacts of the helix formed by residues 22 - 40 (chain B) in PDB entry 2Q9Q
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 THR 22 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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21B LEU* 1.3 85.2 - - + +
23B PRO* 1.3 70.0 - - - +
24B ALA* 3.8 7.5 + - - +
25B GLU* 3.1 37.3 + - - +
26B LEU* 2.8 26.5 + - - +
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Residues in contact with PRO 23 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A ILE* 3.3 32.3 - - + +
21B LEU 4.5 1.1 - - - +
22B THR* 1.3 87.0 - - - +
24B ALA* 1.3 64.0 + - - +
26B LEU* 2.9 21.2 + - + +
27B ILE* 2.9 17.8 + - - +
57B GLN* 3.3 23.8 - - - +
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Residues in contact with ALA 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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29A ILE 3.2 9.0 + - - +
30A GLY* 3.3 30.5 - - - +
31A GLY* 5.2 1.3 - - - -
22B THR* 3.3 7.8 - - - +
23B PRO* 1.3 80.3 - - - +
25B GLU* 1.3 64.4 + - + +
27B ILE* 3.3 5.1 + - - +
28B GLU* 3.1 31.4 + - - +
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Residues in contact with GLU 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 LEU* 2.6 37.1 + - - +
22B THR* 3.1 30.7 + - - +
24B ALA* 1.3 78.6 - - + +
26B LEU* 1.3 65.4 + - - +
28B GLU* 3.2 18.7 + - - +
29B ARG* 3.0 34.7 + - - +
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Residues in contact with LEU 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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21B LEU 5.6 0.4 - - - +
22B THR 2.8 12.4 + - - +
23B PRO* 3.1 12.3 - - + +
25B GLU* 1.3 78.1 - - - +
27B ILE* 1.3 66.2 + - + +
29B ARG* 3.3 7.7 + - + +
30B LEU* 3.1 20.1 + - - +
50B ILE* 4.1 23.8 - - + +
53B CYS* 3.5 52.5 - - + +
54B VAL* 3.9 12.1 - - + +
57B GLN* 3.8 20.4 - - + +
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Residues in contact with ILE 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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12A LYS* 5.0 5.4 - - - +
29A ILE* 4.0 22.0 - - + +
30A GLY* 5.0 4.7 - - - -
23B PRO 2.9 14.3 + - - +
24B ALA* 3.6 7.4 - - - +
26B LEU* 1.3 85.1 - - + +
28B GLU* 1.3 66.2 + - + +
30B LEU* 3.2 9.7 + - + +
31B GLU* 3.0 47.5 + - + +
54B VAL* 4.9 7.2 - - + -
57B GLN* 6.0 1.1 - - + -
85B ILE* 3.5 45.5 - - + -
88B VAL* 6.5 0.2 - - + -
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Residues in contact with GLU 28 (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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12A LYS* 5.2 9.4 - - - +
24B ALA* 3.1 20.3 + - - +
25B GLU* 3.2 21.8 + - - +
27B ILE* 1.3 75.0 - - + +
29B ARG* 1.3 63.8 + - + +
31B GLU* 3.4 10.1 + - - +
32B GLN* 3.0 24.4 + - - +
176B ARG* 6.4 0.4 - - - +
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Residues in contact with ARG 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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25B GLU* 3.0 21.1 + - - +
26B LEU* 3.5 11.7 - - + +
28B GLU* 1.3 77.6 - - - +
30B LEU* 1.3 61.8 + - - +
32B GLN* 3.2 23.9 + - - +
33B ALA* 3.1 22.0 + - - +
50B ILE* 3.6 30.7 - - + +
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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 LEU 3.1 10.4 + - - +
27B ILE* 3.2 14.6 + - + +
29B ARG* 1.3 79.3 - - - +
31B GLU* 1.3 65.1 + - + +
33B ALA* 3.0 8.6 + - + +
34B TRP* 2.9 20.8 + - - +
50B ILE* 4.1 22.0 - - + +
51B VAL* 5.8 0.2 - - + -
54B VAL* 4.3 18.8 - - + -
85B ILE* 4.2 13.2 - - + +
88B VAL* 3.7 28.5 - - + -
89B LEU* 4.0 32.1 - - + +
92B TYR* 4.1 20.4 - - + -
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Residues in contact with GLU 31 (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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8A PHE* 4.3 15.2 - - - -
9A LEU* 4.3 12.2 - - + +
12A LYS* 2.6 45.6 + - - +
27B ILE* 3.0 29.2 + - + +
28B GLU* 3.8 8.0 - - - +
30B LEU* 1.3 75.3 - - + +
32B GLN* 1.3 57.0 + - - +
34B TRP* 3.4 15.7 - - + +
35B MET* 2.9 36.6 + - + +
84B ARG* 5.3 0.5 + - - -
88B VAL* 4.2 16.1 - - + +
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Residues in contact with GLN 32 (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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28B GLU 3.0 12.5 + - - +
29B ARG* 3.3 32.9 + - - +
31B GLU* 1.3 78.3 - - - +
33B ALA* 1.3 57.8 + - - +
36B ASN* 2.9 46.5 + - - +
176B ARG* 3.8 37.6 + - - +
215B VAL 5.3 0.3 - - - +
218B GLY* 3.9 17.7 - - - -
220B VAL 4.8 0.7 - - - +
221B GLN* 2.9 29.2 + - - +
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Residues in contact with ALA 33 (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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29B ARG 3.1 10.6 + - - +
30B LEU* 3.0 11.7 + - + +
32B GLN* 1.3 74.0 - - - +
34B TRP* 1.3 59.9 - - - +
36B ASN* 3.9 5.6 - - - +
37B GLU* 2.8 34.8 + - - +
44B LEU* 5.2 1.1 - - - +
47B LYS* 4.5 17.7 - - + +
50B ILE* 5.3 3.6 - - + -
92B TYR* 3.8 30.4 - - + +
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Residues in contact with TRP 34 (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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1A MET* 4.1 15.3 - - + -
5A GLU* 3.6 25.1 - - + -
8A PHE* 4.0 24.7 - + - -
9A LEU* 4.0 23.6 - - + -
30B LEU 2.9 11.8 + - - +
31B GLU* 3.4 20.4 - - + +
33B ALA* 1.3 77.3 - - - +
35B MET* 1.3 77.0 + - + +
37B GLU* 3.9 1.6 - - - +
38B LYS* 3.1 44.6 + - + +
87B TYR* 4.1 12.6 - + - -
88B VAL* 3.7 26.7 - - + -
91B SER* 2.9 29.2 + - - -
92B TYR* 3.7 32.4 - - + -
95B CYS* 5.5 1.0 - - + +
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Residues in contact with MET 35 (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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1A MET* 3.6 41.5 - - + +
9A LEU* 4.0 20.0 - - + -
150A LEU* 4.5 12.6 - - + -
31B GLU* 2.9 19.3 + - + +
34B TRP* 1.3 89.7 - - + +
36B ASN* 1.3 65.2 + - - +
38B LYS* 3.3 12.1 + - - +
39B PHE* 3.0 41.0 - - + -
221B GLN* 3.2 22.9 - - + +
222B LEU 3.7 8.5 - - - +
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Residues in contact with ASN 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 GLN* 2.9 43.9 + - - +
33B ALA* 3.9 5.8 - - - +
35B MET* 1.3 76.6 - - - +
37B GLU* 1.3 57.0 + - - +
39B PHE 3.4 0.5 + - - -
40B ALA* 2.9 34.1 + - - +
44B LEU* 3.7 16.4 - - + -
215B VAL* 3.5 26.8 + - + +
220B VAL 4.4 4.9 + - - -
221B GLN* 3.6 6.3 + - - +
222B LEU* 2.9 38.6 + - - +
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Residues in contact with GLU 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 ALA 2.8 18.3 + - - +
34B TRP 3.9 3.6 - - - +
36B ASN* 1.3 74.1 - - - +
38B LYS* 1.3 65.8 + - - +
39B PHE 3.3 0.7 + - - -
40B ALA 3.7 0.5 + - - -
43B LEU* 3.9 1.6 - - - +
44B LEU* 3.1 32.2 + - - +
45B GLU 4.7 0.3 - - - +
92B TYR* 3.5 18.8 + - + -
95B CYS* 3.5 17.1 - - + -
96B ARG* 2.9 46.7 + - + +
99B LYS* 2.6 55.8 + - - +
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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
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1A MET* 3.9 29.0 + - + +
5A GLU* 2.9 37.2 + - - -
34B TRP* 3.1 50.2 + - + +
35B MET* 3.4 17.0 - - - +
37B GLU* 1.3 78.8 - - - +
39B PHE* 1.3 72.7 + - + +
40B ALA 4.7 1.6 - - - +
91B SER* 4.0 6.7 + - - -
95B CYS* 3.9 16.5 - - + -
99B LYS* 5.4 0.7 - - - -
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Residues in contact with PHE 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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1A MET* 3.7 42.2 - - + -
150A LEU* 5.8 2.9 - - + -
154A ASN* 4.2 13.5 - - - -
35B MET* 3.0 49.9 + - + -
37B GLU 3.2 0.2 - - - -
38B LYS* 1.3 86.7 - - + +
40B ALA* 1.3 66.9 + - - +
41B PRO* 3.5 5.7 - - - +
171B VAL* 3.8 18.0 - - + +
172B PHE 5.6 1.3 - - - +
222B LEU* 3.7 35.9 - - + -
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Residues in contact with ALA 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 ASN 2.9 18.6 + - - +
37B GLU 3.7 0.8 + - - +
38B LYS 4.7 1.0 - - - +
39B PHE* 1.3 77.8 - - - +
41B PRO* 1.3 66.6 - - + +
42B GLU 3.2 8.5 - - - +
44B LEU* 3.7 31.4 - - + -
99B LYS* 3.0 25.2 + - - +
208B TYR* 4.0 10.3 - - + +
222B LEU* 3.9 7.8 - - + +
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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