Contacts of the helix formed by residues 24 - 43 (chain A) in PDB entry 7BQQ
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 ASP 24 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23A GLN* 1.3 78.7 - - - +
25A PRO* 1.3 74.8 - - + +
26A GLU* 4.6 2.9 - - + +
27A LYS* 3.1 41.1 + - + +
28A VAL 3.5 4.5 + - - -
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Residues in contact with PRO 25 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A GLN 3.7 6.2 - - - +
24A ASP* 1.3 89.0 - - + +
26A GLU* 1.3 70.3 + - + +
28A VAL* 3.5 14.2 + - + +
29A LYS* 3.6 5.0 - - - +
73A TRP* 3.3 46.4 + - + +
74A ARG* 5.6 2.7 - - - +
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Residues in contact with GLU 26 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24A ASP* 3.3 3.3 - - + -
25A PRO* 1.3 84.6 - - + +
27A LYS* 1.3 67.6 + - + +
29A LYS* 2.8 57.7 + - - +
30A GLU* 3.5 13.4 - - - +
74A ARG* 4.4 7.1 + - - -
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Residues in contact with LYS 27 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A GLN* 3.7 11.0 - - + +
24A ASP* 3.1 32.3 + - + +
26A GLU* 1.3 77.7 - - + +
28A VAL* 1.3 64.3 + - - +
30A GLU* 3.0 25.1 + - - +
31A ILE* 2.9 32.4 + - + +
119A GLU* 5.6 6.5 + - - -
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Residues in contact with VAL 28 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A MET* 3.5 25.8 - - + -
23A GLN* 3.4 30.2 + - + +
24A ASP 3.8 8.7 - - - +
25A PRO* 3.5 15.5 - - + +
26A GLU 3.4 0.2 - - - -
27A LYS* 1.3 75.8 - - - +
29A LYS* 1.3 56.3 + - - +
31A ILE* 3.2 6.9 + - - +
32A VAL* 2.9 35.1 + - + +
73A TRP* 3.3 42.0 - - + -
76A MET* 3.7 10.5 - - + -
80A ARG* 5.6 0.4 - - - +
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Residues in contact with LYS 29 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25A PRO 3.6 13.0 - - - +
26A GLU* 2.8 47.5 + - - +
27A LYS 3.2 0.6 - - - -
28A VAL* 1.3 74.5 - - - +
30A GLU* 1.3 57.3 + - + +
32A VAL* 3.5 4.8 + - - -
33A ARG* 2.9 35.9 + - - +
66A LYS 5.9 1.3 - - - +
69A ALA* 3.5 15.8 - - + +
70A GLU* 2.8 44.5 + - + +
73A TRP* 3.6 18.6 - - + -
74A ARG* 4.1 2.7 - - - +
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Residues in contact with GLU 30 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26A GLU 3.5 15.7 - - - +
27A LYS* 3.0 27.7 + - - +
29A LYS* 1.3 73.3 - - + +
31A ILE* 1.3 61.9 + - - +
33A ARG* 2.8 54.2 + - - +
34A ARG* 3.0 32.4 + - - +
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Residues in contact with ILE 31 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20A MET* 5.3 2.5 - - + -
23A GLN* 3.1 35.0 - - - +
27A LYS* 2.9 22.5 + - + +
28A VAL* 3.6 7.0 - - - +
30A GLU* 1.3 74.6 - - - +
32A VAL* 1.3 63.6 + - - +
34A ARG* 3.3 28.5 - - - +
35A ALA* 3.1 22.9 + - - +
112A MET* 4.2 9.6 - - + +
115A VAL* 4.0 18.2 - - + -
116A GLN* 3.8 30.3 - - + +
119A GLU* 4.4 15.9 - - + +
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Residues in contact with VAL 32 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20A MET* 5.5 0.2 - - + -
28A VAL* 2.9 24.4 + - + +
29A LYS* 3.8 4.3 - - - +
31A ILE* 1.3 71.5 - - - +
33A ARG* 1.3 58.7 + - - +
35A ALA* 3.2 7.4 + - - -
36A LEU* 2.8 37.1 + - + +
69A ALA* 3.5 33.2 - - + +
72A VAL* 3.7 22.7 - - + -
73A TRP* 4.8 2.2 - - + +
76A MET* 3.8 28.3 - - + -
108A PHE* 4.1 7.4 - - + -
112A MET* 4.7 10.1 - - + -
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Residues in contact with ARG 33 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29A LYS* 2.9 21.0 + - - +
30A GLU* 2.8 58.0 + - - +
31A ILE 3.3 0.2 - - - -
32A VAL* 1.3 75.8 - - - +
34A ARG* 1.3 58.2 + - + +
36A LEU* 3.6 0.3 - - - +
37A GLN* 3.0 24.9 + - - +
62A SER 5.7 0.4 - - - -
65A ILE* 3.1 36.5 - - + +
66A LYS* 3.8 40.3 - - - +
69A ALA* 3.6 11.4 - - + +
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Residues in contact with ARG 34 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30A GLU* 3.0 28.6 + - - +
31A ILE* 3.3 27.7 - - - +
33A ARG* 1.3 76.7 - - + +
35A ALA* 1.3 57.9 + - - +
37A GLN* 3.5 11.4 - - + +
38A GLN* 3.0 28.6 + - - +
115A VAL* 3.8 31.2 + - + +
118A LYS* 6.3 0.2 - - - +
119A GLU* 2.8 45.7 + - - +
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Residues in contact with ALA 35 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31A ILE 3.1 18.7 + - - +
32A VAL* 3.2 3.1 + - - +
34A ARG* 1.3 77.0 - - - +
36A LEU* 1.3 60.8 + - - +
38A GLN* 3.5 14.6 + - - +
39A MET* 4.1 3.3 + - - +
108A PHE* 3.5 26.1 - - + -
111A ILE* 4.0 15.9 - - + +
112A MET* 3.7 30.5 - - + +
115A VAL* 4.1 5.8 - - + -
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Residues in contact with LEU 36 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32A VAL* 2.8 22.2 + - + +
33A ARG 3.6 4.5 - - - +
35A ALA* 1.3 71.3 - - - +
37A GLN* 1.3 64.3 + - - +
39A MET* 3.5 24.9 + - - +
40A ALA* 4.2 2.3 + - - +
46A VAL* 4.9 1.6 - - - +
50A LEU* 5.0 1.9 - - + +
65A ILE* 3.8 26.7 - - + +
68A LEU* 3.7 22.4 - - + +
69A ALA* 3.4 41.5 - - + +
94A PHE* 4.0 14.4 - - + -
98A LEU* 4.0 21.7 - - + +
108A PHE* 3.5 19.0 - - + -
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Residues in contact with GLN 37 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33A ARG 3.0 21.2 + - - +
34A ARG* 3.5 11.7 - - + +
36A LEU* 1.3 78.7 - - - +
38A GLN* 1.3 61.8 + - - +
39A MET 3.3 0.2 - - - -
40A ALA* 3.1 13.2 + - - +
41A ASN* 2.9 36.9 + - - +
50A LEU* 3.8 24.2 - - - +
61A PRO 5.5 0.2 + - - -
62A SER* 4.5 12.3 - - - -
65A ILE* 4.1 20.5 - - + +
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Residues in contact with GLN 38 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34A ARG 3.0 17.4 + - - +
35A ALA 3.6 8.1 - - - +
36A LEU 3.4 0.4 - - - -
37A GLN* 1.3 74.9 - - - +
39A MET* 1.3 58.0 + - - +
41A ASN* 3.0 16.9 + - - +
42A ASP* 2.8 45.9 + - + +
111A ILE* 3.7 35.5 - - + +
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Residues in contact with MET 39 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35A ALA 4.1 2.2 + - - +
36A LEU 3.5 16.3 + - - +
37A GLN 3.3 0.6 - - - -
38A GLN* 1.3 77.9 - - - +
40A ALA* 1.3 55.7 + - - +
42A ASP* 4.4 2.0 - - - -
43A ASN* 2.9 44.3 + - - +
46A VAL* 3.7 15.1 - - + +
94A PHE* 4.5 4.9 - - + -
98A LEU* 4.4 10.5 - - + -
100A ILE* 3.6 26.2 - - + -
104A GLN* 3.7 39.7 - - - +
107A LYS* 4.7 5.8 - - + -
108A PHE* 3.6 31.2 - - + -
111A ILE* 4.4 14.6 - - + -
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Residues in contact with ALA 40 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36A LEU 4.2 0.6 + - - +
37A GLN* 3.1 14.7 + - - +
39A MET* 1.3 74.9 - - - +
41A ASN* 1.3 63.3 + - - +
43A ASN 3.2 21.1 - - - +
44A PRO* 4.8 0.3 - - - +
46A VAL* 3.9 8.8 - - + +
47A SER* 3.6 27.3 + - - +
50A LEU* 3.3 34.1 - - + -
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Residues in contact with ASN 41 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37A GLN* 2.9 45.8 + - - +
38A GLN* 3.0 22.4 + - - +
40A ALA* 1.3 76.7 - - - +
42A ASP* 1.3 58.5 + - - +
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Residues in contact with ASP 42 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38A GLN* 2.8 32.2 + - + +
39A MET* 4.4 1.3 - - - -
41A ASN* 1.3 77.1 - - - +
43A ASN* 1.3 81.9 + - - +
44A PRO* 4.5 3.2 - - - +
107A LYS* 4.9 10.7 + - - +
111A ILE* 6.4 0.2 - - + -
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Residues in contact with ASN 43 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39A MET* 2.9 38.4 + - - +
40A ALA 3.2 14.9 - - - +
41A ASN 3.6 0.2 - - - -
42A ASP* 1.3 103.2 + - - +
44A PRO* 1.3 70.0 - - + +
45A GLU* 3.4 17.9 + - + +
46A VAL* 3.5 20.0 + - + +
47A SER 3.5 3.5 + - - -
104A GLN* 4.8 7.4 - - - +
107A LYS* 5.5 9.0 + - - +
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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
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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