Contacts of the helix formed by residues 21 - 42 (chain A) in PDB entry 4BHT
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 GLN 21 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15A GLN* 5.5 1.3 + - - -
18A ASP* 3.1 41.9 + - + +
19A PRO 3.7 0.9 - - - -
20A ASN* 1.3 76.9 - - - +
22A THR* 1.3 61.9 + - - +
24A PHE* 3.4 11.0 + - + +
25A ALA* 3.1 22.2 + - - +
103A LEU* 3.7 34.6 - - - +
104A SER* 3.2 28.7 - - - +
107A LYS* 3.0 32.2 + - - +
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Residues in contact with THR 22 (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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15A GLN* 6.2 0.7 - - - +
20A ASN* 3.1 12.2 + - - -
21A GLN* 1.3 72.6 - - - +
23A GLU* 1.3 74.8 + - + +
25A ALA* 3.4 5.8 + - - +
26A GLN* 3.2 21.2 + - + +
104A SER* 3.4 2.0 + - - -
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Residues in contact with GLU 23 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A THR* 1.3 84.5 + - + +
24A PHE* 1.3 64.9 + - - +
26A GLN* 3.2 8.7 + - - +
27A ALA* 3.1 20.6 + - - +
102A ASN* 4.4 5.0 + - - +
104A SER* 2.6 33.4 + - - +
105A ILE* 3.5 30.3 - - + +
108A PHE* 3.9 29.6 - - + +
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Residues in contact with PHE 24 (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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14A VAL* 4.8 12.8 - - + -
18A ASP* 4.4 7.4 - - + -
21A GLN* 3.8 30.3 - - + +
22A THR 3.3 0.4 - - - -
23A GLU* 1.3 79.6 - - - +
25A ALA* 1.3 63.9 + - - +
27A ALA* 3.2 3.1 + - + +
28A VAL* 3.0 47.0 + - + +
55A VAL* 3.3 27.8 - - + -
84A PHE* 3.9 19.3 - + - -
104A SER* 3.4 15.0 + - - +
107A LYS* 3.6 44.4 - - + -
108A PHE* 3.9 8.7 - - - -
111A PHE* 4.1 8.7 - + + -
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Residues in contact with ALA 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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11A LEU* 5.4 0.5 - - - +
15A GLN* 4.1 27.6 - - + +
18A ASP 5.9 0.7 - - - +
21A GLN 3.1 12.9 + - - +
22A THR* 3.7 9.9 - - - +
24A PHE* 1.3 78.8 - - - +
26A GLN* 1.3 57.8 + - - +
28A VAL* 3.3 6.4 + - - +
29A ARG* 2.9 31.8 + - - +
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Residues in contact with GLN 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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22A THR* 3.2 10.2 + - + +
23A GLU* 3.2 11.9 + - - +
25A ALA* 1.3 79.0 - - - +
27A ALA* 1.3 57.7 + - - +
29A ARG* 3.3 22.0 + - - +
30A GLU* 2.9 36.8 + - + +
353A ILE* 4.5 23.6 - - + +
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Residues in contact with ALA 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 GLU 3.1 7.8 + - - +
24A PHE* 3.6 8.1 - - + +
26A GLN* 1.3 75.5 - - - +
28A VAL* 1.3 62.0 + - - +
30A GLU* 3.4 5.5 + - - +
31A VAL* 3.1 28.9 + - + +
108A PHE* 3.6 37.7 - - + +
111A PHE* 4.2 17.5 - - + -
112A GLU* 5.2 4.0 - - + +
370A LYS* 5.3 2.1 + - - +
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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
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10A PHE* 4.6 2.5 - - + -
11A LEU* 3.6 20.6 - - + -
14A VAL* 4.5 14.6 - - + -
24A PHE* 3.0 51.3 + - + +
25A ALA* 3.7 5.6 - - - +
27A ALA* 1.3 71.1 - - - +
29A ARG* 1.3 60.0 + - - +
31A VAL* 3.9 0.3 - - - +
32A MET* 2.9 45.9 + - + +
55A VAL* 4.4 16.6 - - + -
111A PHE* 4.0 17.9 - - + -
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Residues in contact with ARG 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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7A LEU* 4.8 5.5 - - - +
8A GLU* 3.0 40.8 + - - -
11A LEU* 3.2 39.5 - - + +
25A ALA 2.9 18.5 + - - +
26A GLN* 3.6 20.9 - - - +
28A VAL* 1.3 76.5 - - - +
30A GLU* 1.3 61.5 + - - +
32A MET* 4.0 0.2 - - - +
33A THR* 2.8 44.3 + - - +
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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 GLN* 2.9 25.2 + - + +
27A ALA* 3.8 5.8 - - - +
29A ARG* 1.3 82.2 - - - +
31A VAL* 1.3 64.2 + - - +
33A THR* 3.9 8.0 + - - +
34A THR* 3.4 26.7 + - - -
353A ILE* 4.6 24.2 - - + +
370A LYS* 4.3 17.9 - - - +
426A VAL* 4.7 11.8 - - + +
430A ASN* 4.0 3.5 + - - +
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Residues in contact with VAL 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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27A ALA 3.1 17.9 + - - +
28A VAL 4.0 2.7 - - - +
30A GLU* 1.3 73.5 - - - +
32A MET* 1.3 76.1 + - + +
34A THR* 3.0 14.6 + - - -
35A LEU* 3.0 35.6 + - + +
111A PHE* 3.8 24.5 - - + -
112A GLU* 6.4 1.8 - - + -
115A PHE* 4.5 20.9 - - + -
370A LYS* 4.1 17.7 - - - +
430A ASN* 4.1 18.1 + - + +
434A PHE* 5.9 0.4 - - + -
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Residues in contact with MET 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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7A LEU* 3.6 20.0 - - + -
10A PHE* 3.8 26.7 - - + -
11A LEU* 4.0 3.6 - - + -
28A VAL* 2.9 25.8 + - + +
29A ARG 4.0 1.3 - - - +
31A VAL* 1.3 89.0 - - + +
33A THR* 1.3 63.5 + - - +
35A LEU* 4.2 15.5 - - + +
36A TRP* 3.0 43.7 + - + +
51A LEU* 4.2 22.0 - - + -
54A LEU* 4.7 5.8 - - + -
55A VAL* 3.7 28.9 - - + -
111A PHE* 4.6 6.1 - - + -
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Residues in contact with THR 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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7A LEU* 3.7 27.4 - - + +
29A ARG* 2.8 38.5 + - - +
30A GLU* 3.9 11.8 + - - +
31A VAL 3.2 0.4 - - - -
32A MET* 1.3 74.7 - - - +
34A THR* 1.3 63.2 + - - +
36A TRP* 3.6 7.2 + - - +
37A PRO* 3.6 10.6 - - - +
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Residues in contact with THR 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* 3.4 11.0 + - - -
31A VAL 3.0 4.9 + - - -
33A THR* 1.3 80.8 - - - +
35A LEU* 1.3 60.0 + - - +
37A PRO* 3.8 8.7 - - - +
38A PHE 4.6 1.0 + - - -
426A VAL* 4.3 10.0 - - - +
427A GLN* 3.4 43.4 - - + +
430A ASN* 3.3 36.0 + - + +
431A ILE* 4.4 10.3 - - + +
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Residues in contact with LEU 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 VAL* 3.0 37.5 + - + +
32A MET* 3.2 17.9 + - + +
34A THR* 1.3 77.6 - - - +
36A TRP* 1.3 68.3 + - - +
37A PRO 3.2 0.4 - - - -
38A PHE* 2.8 12.9 + - + +
39A LEU* 2.8 34.5 + - + +
51A LEU* 5.0 0.2 - - + -
430A ASN* 4.1 5.4 - - + +
431A ILE* 3.8 26.7 - - + +
434A PHE* 3.7 56.3 - - + -
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Residues in contact with TRP 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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6A SER* 3.5 31.2 - - - +
7A LEU* 3.4 36.9 - - + +
10A PHE* 3.8 29.4 - + + -
32A MET* 3.0 34.1 + - + +
33A THR* 4.1 4.0 - - - +
35A LEU* 1.3 76.2 - - - +
37A PRO* 1.3 65.8 - - + +
39A LEU* 3.2 12.1 + - + +
40A GLU* 3.0 57.5 + - - +
46A ARG* 3.1 33.4 - - - +
51A LEU* 3.8 21.5 - - + -
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Residues in contact with PRO 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 THR 3.6 12.8 - - - +
34A THR 3.8 5.8 - - - +
35A LEU 3.5 2.9 - - - -
36A TRP* 1.3 92.1 - - + +
38A PHE* 1.3 63.2 + - - +
40A GLU* 3.3 17.0 + - + +
41A GLN* 3.2 25.4 + - - +
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Residues in contact with PHE 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 THR 4.6 0.8 + - - -
35A LEU* 2.8 16.8 + - + +
37A PRO* 1.3 74.2 - - - +
39A LEU* 1.3 66.8 + - + +
41A GLN* 3.0 5.2 + - - -
42A ASN* 2.8 57.5 + - - +
45A TYR* 3.6 31.2 - + - -
416A HIS* 4.3 14.6 - + - -
431A ILE* 3.6 45.5 - - + -
434A PHE* 4.1 12.3 - + - -
435A VAL* 3.5 27.1 - - + -
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Residues in contact with LEU 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 LEU* 2.8 35.7 + - + +
36A TRP* 3.5 11.4 - - + +
38A PHE* 1.3 74.1 - - + +
40A GLU* 1.3 66.4 + - - +
42A ASN 3.1 21.5 + - - +
43A PRO* 3.4 6.2 - - - +
45A TYR* 3.6 42.0 - - + +
46A ARG* 3.3 30.9 + - + +
51A LEU* 3.8 30.3 - - + -
434A PHE* 3.9 17.0 - - + -
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Residues in contact with GLU 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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6A SER 5.9 0.3 + - - -
36A TRP* 3.0 39.7 + - - +
37A PRO* 3.6 16.7 - - - +
39A LEU* 1.3 76.8 - - - +
41A GLN* 1.3 72.2 + - - +
43A PRO* 3.9 9.0 - - - +
46A ARG* 4.2 11.0 - - - +
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Residues in contact with GLN 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 PRO 3.2 11.1 + - - +
38A PHE* 3.0 10.6 + - - +
40A GLU* 1.3 88.5 + - - +
42A ASN* 1.3 68.9 + - - +
43A PRO* 3.5 7.8 - - - +
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Residues in contact with ASN 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 PHE* 2.8 55.0 + - + +
39A LEU* 3.1 7.8 + - - +
41A GLN* 1.3 92.7 + - - +
43A PRO* 1.4 53.4 - - - +
44A LYS* 2.9 18.8 + - + -
45A TYR* 2.9 38.4 + - + +
46A ARG 4.4 0.7 + - - -
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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