Contacts of the helix formed by residues 21 - 42 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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18B ASP* 3.1 40.9 + - + +
19B PRO 3.7 1.3 - - - -
20B ASN* 1.3 74.1 - - - +
22B THR* 1.3 58.5 + - - +
24B PHE* 3.3 9.4 + - + +
25B ALA* 2.9 29.3 + - - +
103B LEU* 3.7 33.7 - - - +
104B SER* 3.3 29.6 - - - +
107B LYS* 2.9 32.5 + - - +
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Residues in contact with THR 22 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B ASN* 3.2 10.4 + - - -
21B GLN* 1.3 72.4 - - - +
23B GLU* 1.3 75.2 + - + +
25B ALA* 3.3 7.2 + - - +
26B GLN* 2.9 24.6 + - + +
104B SER* 3.5 2.0 + - - -
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Residues in contact with GLU 23 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B THR* 1.3 85.4 + - + +
24B PHE* 1.3 64.1 + - - +
26B GLN* 3.3 7.0 + - - +
27B ALA* 3.0 24.6 + - - +
102B ASN* 4.5 5.1 + - - +
104B SER* 2.7 33.8 + - - +
105B ILE* 3.6 30.2 - - + +
108B PHE* 3.7 27.2 - - + +
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Residues in contact with PHE 24 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14B VAL* 4.5 13.5 - - + -
18B ASP* 4.3 9.0 - - + -
21B GLN* 3.6 31.4 - - + +
22B THR 3.2 0.2 - - - -
23B GLU* 1.3 80.1 - - - +
25B ALA* 1.3 65.5 - - - +
27B ALA* 3.2 3.2 + - + +
28B VAL* 3.0 49.0 + - + +
55B VAL* 3.5 25.8 - - + -
84B PHE* 4.2 10.1 - + - -
104B SER* 3.2 14.5 + - - +
107B LYS* 3.6 49.8 - - + -
108B PHE* 3.9 8.1 - - - -
111B PHE* 4.3 7.6 - + + -
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Residues in contact with ALA 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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11B LEU* 5.5 0.5 - - - +
14B VAL* 6.2 2.2 - - - -
15B GLN* 4.5 25.1 - - + +
18B ASP 5.6 2.5 - - - +
21B GLN 2.9 17.2 + - - +
22B THR* 3.6 6.5 - - - +
24B PHE* 1.3 80.8 - - - +
26B GLN* 1.3 63.2 + - - +
28B VAL* 3.4 6.4 + - - +
29B ARG* 3.0 23.9 + - - +
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Residues in contact with GLN 26 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B THR* 2.9 18.9 + - + +
23B GLU* 3.7 7.0 - - - +
24B PHE 3.2 0.2 - - - -
25B ALA* 1.3 76.8 - - - +
27B ALA* 1.3 63.7 + - - +
29B ARG* 3.3 22.9 + - - +
30B GLU* 3.0 30.6 + - + +
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Residues in contact with ALA 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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23B GLU 3.0 11.0 + - - +
24B PHE* 3.6 4.7 - - + +
26B GLN* 1.3 78.4 - - - +
28B VAL* 1.3 61.0 + - - +
30B GLU* 3.6 5.1 + - - +
31B VAL* 3.3 29.1 + - - +
108B PHE* 3.5 41.5 - - + +
111B PHE* 4.3 11.9 - - + -
112B GLU* 4.6 9.7 - - - +
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Residues in contact with VAL 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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10B PHE* 4.5 2.7 - - + -
11B LEU* 3.9 17.0 - - + -
14B VAL* 4.4 13.9 - - + -
24B PHE* 3.0 53.1 + - + +
25B ALA* 3.9 5.8 - - - +
27B ALA* 1.3 70.9 - - - +
29B ARG* 1.3 64.2 + - - +
31B VAL* 3.5 1.6 + - - +
32B MET* 3.0 40.1 + - + +
55B VAL* 4.2 18.8 - - + -
111B PHE* 3.9 16.2 - - + -
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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
----------------------------------------------------------
7B LEU* 5.1 1.6 - - - +
8B GLU* 3.0 40.8 + - - -
11B LEU* 3.4 38.2 - - + +
12B ASN* 5.8 1.2 - - - +
25B ALA 3.0 14.3 + - - +
26B GLN* 3.3 26.2 + - - +
28B VAL* 1.3 77.4 - - - +
30B GLU* 1.3 59.5 + - - +
32B MET* 3.8 0.7 - - - +
33B THR* 2.8 46.0 + - - +
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Residues in contact with GLU 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 GLN* 3.0 24.6 + - + +
27B ALA* 4.0 5.8 - - - +
29B ARG* 1.3 78.5 - - - +
31B VAL* 1.3 65.2 + - + +
33B THR* 3.6 6.5 + - - +
34B THR* 3.1 37.7 + - - +
112B GLU* 5.7 5.4 - - - +
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Residues in contact with VAL 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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27B ALA 3.3 16.6 + - - +
28B VAL 3.9 3.1 - - - +
30B GLU* 1.3 78.4 - - + +
32B MET* 1.3 68.5 + - + +
34B THR* 3.2 8.2 + - - -
35B LEU* 3.1 43.4 + - + +
111B PHE* 3.6 29.2 - - + -
112B GLU* 5.2 10.5 - - + +
115B PHE* 4.5 19.3 - - + -
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Residues in contact with MET 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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7B LEU* 3.5 20.9 - - + -
10B PHE* 3.7 28.3 - - + -
11B LEU* 4.3 2.7 - - + -
28B VAL* 3.0 23.5 + - + +
29B ARG 4.0 1.1 - - - +
31B VAL* 1.3 82.7 - - + +
33B THR* 1.3 58.0 + - - +
35B LEU* 4.4 12.3 - - + -
36B TRP* 2.9 45.0 + - + +
39B LEU* 5.0 0.4 - - - -
51B LEU* 4.3 24.9 - - + -
54B LEU* 4.5 10.5 - - + -
55B VAL* 3.8 28.7 - - + -
111B PHE* 4.4 15.3 - - + -
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Residues in contact with THR 33 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B LEU* 3.7 26.1 - - + +
29B ARG* 2.8 37.0 + - - +
30B GLU* 3.9 9.2 - - - +
32B MET* 1.3 78.1 - - - +
34B THR* 1.3 62.7 + - - +
36B TRP* 3.7 7.1 + - - +
37B PRO* 3.8 9.4 - - - +
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Residues in contact with THR 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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30B GLU* 3.1 24.5 + - - +
31B VAL* 3.2 11.7 + - - -
33B THR* 1.3 81.8 - - - +
35B LEU* 1.3 63.0 + - + +
37B PRO* 3.9 7.4 - - - +
38B PHE* 5.2 1.9 + - - +
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Residues in contact with LEU 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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31B VAL* 3.1 37.2 + - + +
32B MET* 4.0 16.8 - - + +
33B THR 3.3 0.2 - - - -
34B THR* 1.3 79.0 - - + +
36B TRP* 1.3 67.1 + - - +
37B PRO* 3.3 3.4 - - - -
38B PHE* 2.9 34.8 + - + +
39B LEU* 3.0 31.1 + - + +
51B LEU* 5.5 3.1 - - + -
54B LEU* 5.6 6.3 - - + -
115B PHE* 5.9 3.4 - - + -
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Residues in contact with TRP 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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6B SER* 3.6 13.9 - - - +
7B LEU* 3.4 59.2 - - + +
10B PHE* 4.1 16.4 - + + -
32B MET* 2.9 34.6 + - + +
33B THR* 4.0 6.5 - - - +
34B THR 3.5 0.2 - - - -
35B LEU* 1.3 75.9 - - - +
37B PRO* 1.3 72.1 - - + +
39B LEU* 3.2 12.2 + - + +
40B GLU* 3.1 49.4 + - - +
46B ARG* 3.4 34.3 - - - +
51B LEU* 3.8 25.1 - - + -
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Residues in contact with PRO 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 THR 3.8 11.0 - - - +
34B THR 3.9 7.2 - - - +
35B LEU 3.5 3.4 - - - -
36B TRP* 1.3 95.9 - - + +
38B PHE* 1.3 62.2 + - - +
40B GLU* 3.2 21.1 + - - +
41B GLN* 3.3 19.0 + - + +
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Residues in contact with PHE 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 THR 5.2 1.7 + - - +
35B LEU* 2.9 25.2 + - + +
37B PRO* 1.3 79.3 - - - +
39B LEU* 1.3 75.4 + - + +
41B GLN* 3.2 4.8 + - - -
42B ASN* 2.7 52.4 + - + +
45B TYR* 3.6 44.2 - + + -
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Residues in contact with LEU 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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32B MET* 5.0 0.9 - - - -
35B LEU* 3.0 34.0 + - + +
36B TRP* 3.2 32.1 + - + +
38B PHE* 1.3 83.8 - - + +
40B GLU* 1.3 63.5 + - - +
42B ASN 3.1 23.0 + - - +
43B PRO* 3.7 4.2 - - - +
45B TYR* 3.6 37.5 - - + +
46B ARG* 3.8 23.0 + - + +
51B LEU* 3.9 29.8 - - + -
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Residues in contact with GLU 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 TRP* 3.1 33.9 + - + +
37B PRO* 3.2 14.5 + - - +
39B LEU* 1.3 76.8 - - - +
41B GLN* 1.3 67.9 + - - +
42B ASN 3.5 0.2 + - - -
43B PRO* 4.1 8.0 - - - +
46B ARG* 3.9 16.2 - - - +
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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
----------------------------------------------------------
37B PRO* 3.6 13.0 + - + +
38B PHE* 3.2 5.0 + - - +
40B GLU* 1.3 83.6 + - - +
42B ASN* 1.3 74.4 - - - +
43B PRO* 3.7 7.3 - - - +
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Residues in contact with ASN 42 (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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38B PHE* 2.7 56.1 + - + +
39B LEU 3.1 8.8 + - - +
41B GLN* 1.3 93.2 - - - +
43B PRO* 1.3 59.8 - - - +
44B LYS* 2.8 15.6 + - + +
45B TYR* 2.9 33.5 + - + +
46B ARG 4.2 0.5 + - - -
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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
------------------------------------------------------------
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