Contacts of the helix formed by residues 24 - 37 (chain B) in PDB entry 3HOT
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 24 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22B LYS 4.9 3.4 - - - +
23B LYS* 1.3 78.4 - - - +
25B ALA* 1.3 68.9 + - - +
26B ALA* 4.3 1.0 - - - +
27B GLU* 3.1 53.2 + - - +
28B SER* 3.2 9.7 + - - -
50B PHE* 3.4 5.1 - - - -
30F A 4.5 7.6 + - - +
31F A 3.5 23.8 + - - +
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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
----------------------------------------------------------
24B THR* 1.3 70.5 - - - +
26B ALA* 1.3 59.6 + - - +
27B GLU 2.8 9.7 + - - -
28B SER* 2.8 17.2 + - - -
29B HIS* 3.4 8.3 + - - +
46B CYS* 4.2 10.6 - - + +
47B GLU* 4.0 36.3 - - + +
50B PHE* 3.3 30.5 - - + -
31F A 3.6 14.4 + - - +
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Residues in contact with ALA 26 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B THR* 4.5 0.2 - - - +
25B ALA* 1.3 71.7 - - - +
27B GLU* 1.3 60.1 + - - +
29B HIS* 3.7 4.7 + - - +
30B ARG* 3.5 24.8 + - - +
43B VAL* 3.9 26.3 - - + +
47B GLU* 5.3 1.8 - - - +
30F A 3.6 34.7 + - + +
31F A 2.9 22.8 + - - +
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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
----------------------------------------------------------
22B LYS 4.8 1.7 - - - +
23B LYS* 4.0 24.8 - - + +
24B THR* 3.1 51.5 + - - +
25B ALA 2.8 0.2 + - - -
26B ALA* 1.3 78.4 - - - +
28B SER* 1.3 61.6 + - - +
30B ARG* 3.3 49.8 + - - +
31B MET* 3.7 12.5 + - - +
30F A 4.5 12.0 + - - +
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Residues in contact with SER 28 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A PHE* 5.6 0.3 - - - -
15B LEU* 4.6 15.3 - - - -
18B CYS* 2.9 37.9 + - - +
23B LYS* 3.6 8.7 - - - +
24B THR 3.2 10.5 + - - -
25B ALA 2.8 9.1 + - - -
27B GLU* 1.3 75.3 - - - +
29B HIS* 1.3 60.6 + - - +
30B ARG 3.3 0.2 - - - -
31B MET* 3.4 11.6 + - - +
32B LEU* 2.9 30.6 + - - +
46B CYS* 5.7 1.1 - - - -
50B PHE* 4.2 5.3 - - - -
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Residues in contact with HIS 29 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B ALA 3.4 8.0 + - - +
26B ALA 3.9 8.5 - - - +
27B GLU 3.2 0.8 - - - -
28B SER* 1.3 76.2 - - - +
30B ARG* 1.3 62.2 + - + +
32B LEU* 3.1 9.1 + - + +
33B VAL* 2.8 50.2 + - + +
38B GLU* 5.6 2.2 + - - +
40B VAL* 4.1 9.3 - - + +
41B PRO 3.0 28.7 + - - -
42B THR* 3.9 2.7 - - - -
43B VAL* 3.5 37.5 + - + -
46B CYS* 4.2 10.6 - - - -
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Residues in contact with ARG 30 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B LYS* 5.7 2.4 - - - +
26B ALA 3.5 12.1 + - - +
27B GLU* 3.3 44.3 + - - +
28B SER 3.3 0.2 - - - -
29B HIS* 1.3 81.0 - - + +
31B MET* 1.3 62.1 + - + +
33B VAL* 3.4 7.9 + - - +
34B GLU* 3.2 21.9 + - - +
30F A 5.0 10.3 + - - -
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Residues in contact with MET 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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17A PHE* 3.9 31.6 - - + -
21A LEU* 4.2 17.1 - - + +
31A MET* 5.6 3.1 - - + -
18B CYS* 3.9 14.8 - - - -
21B LEU* 5.0 8.1 - - + -
23B LYS* 3.8 41.3 - - + +
27B GLU 3.7 8.5 - - - +
28B SER* 3.4 21.1 + - - +
29B HIS 3.2 0.2 - - - -
30B ARG* 1.3 72.9 - - + +
32B LEU* 1.3 61.3 + - - +
34B GLU* 3.1 17.8 + - - +
35B ALA* 2.9 32.6 + - - +
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Residues in contact with LEU 32 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A PHE* 4.4 4.9 - - + -
11B THR* 5.1 9.9 - - + +
14B VAL* 4.4 19.5 - - + -
15B LEU* 3.6 26.9 - - + -
28B SER 2.9 16.7 + - - +
29B HIS* 3.1 9.4 + - - +
31B MET* 1.3 76.1 - - - +
33B VAL* 1.3 61.1 + - - +
35B ALA* 4.7 0.4 - - - +
36B PHE* 3.2 55.4 + - + +
37B GLY 3.8 2.1 - - - +
40B VAL* 3.9 29.6 - - + +
41B PRO* 4.8 9.9 - - + -
46B CYS* 4.6 14.1 - - - -
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Residues in contact with VAL 33 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29B HIS* 2.8 42.4 + - + +
30B ARG* 3.6 7.6 - - - +
32B LEU* 1.3 77.8 - - - +
34B GLU* 1.3 60.6 + - + +
37B GLY* 2.8 49.1 + - - +
38B GLU* 4.6 25.6 - - + +
40B VAL* 4.7 4.0 - - + -
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Residues in contact with GLU 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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20A HIS 3.8 6.9 - - - +
21A LEU* 4.7 24.7 - - + +
30B ARG 3.2 11.4 + - - +
31B MET* 3.1 22.6 + - - +
33B VAL* 1.3 80.2 - - + +
35B ALA* 1.3 64.3 + - - +
37B GLY 4.6 0.7 + - - -
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Residues in contact with ALA 35 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A PHE* 3.8 7.4 - - + -
20A HIS* 3.4 27.2 + - + +
21A LEU* 3.4 29.4 - - + -
31B MET 2.9 13.2 + - - +
32B LEU 4.3 1.1 - - - +
34B GLU* 1.3 81.1 - - - +
36B PHE* 1.3 85.3 + - + +
37B GLY 3.6 1.3 + - - -
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Residues in contact with PHE 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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13A THR* 5.5 0.9 - - + -
16A ILE* 4.3 7.4 - - + -
17A PHE* 3.4 45.1 - + + -
20A HIS* 3.3 30.5 - + - -
5B VAL* 5.1 3.8 - - - -
6B PRO* 3.6 46.3 - - + +
11B THR* 6.5 0.2 - - - -
14B VAL* 4.4 10.1 - - + -
32B LEU* 3.2 32.2 + - + +
35B ALA* 1.3 91.1 - - + +
37B GLY* 1.3 67.5 + - - +
39B GLN* 3.5 17.5 - - - +
40B VAL* 4.0 4.2 - - + +
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Residues in contact with GLY 37 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32B LEU 3.8 1.7 - - - +
33B VAL* 2.8 34.7 + - - +
34B GLU 4.5 1.2 + - - -
35B ALA 3.6 3.2 + - - -
36B PHE* 1.3 81.4 - - - +
38B GLU* 1.3 60.3 + - - -
39B GLN* 3.1 7.3 + - - -
40B VAL* 4.1 2.9 - - - +
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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