Contacts of the helix formed by residues 32 - 45 (chain B) in PDB entry 3Q19
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 CYS 32 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29B MET* 3.0 22.9 + - + +
31B PHE* 1.3 75.9 - - - +
33B PRO* 1.4 65.8 - - - +
34B TYR* 3.7 10.1 - - - -
35B SER* 3.2 22.4 + - - +
36B HIS* 3.1 21.5 + - - +
39B ARG* 4.9 1.2 + - - -
72B ILE* 3.8 12.8 - - + -
184B ARG* 3.5 1.0 + - - -
240B GSH 2.0 53.2 - - - -
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Residues in contact with PRO 33 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31B PHE 3.5 8.5 - - - +
32B CYS* 1.4 80.7 - - - +
34B TYR* 1.3 70.7 + - + +
36B HIS* 3.3 1.2 + - + -
37B ARG* 3.2 16.6 + - - +
180B PRO* 3.3 19.5 - - + +
181B TRP* 3.5 43.2 - - + +
184B ARG* 3.4 30.7 - - - +
188B TYR* 5.3 4.3 - - - +
240B GSH 3.9 10.1 - - - -
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Residues in contact with TYR 34 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32B CYS* 3.3 5.7 - - - -
33B PRO* 1.3 82.3 - - + +
35B SER* 1.3 60.5 + - - +
37B ARG* 3.2 37.2 - - - +
38B THR* 3.7 1.4 + - - -
73B PRO* 4.0 4.9 - - + -
86B SER* 3.3 11.9 - - - +
124B PRO* 3.4 22.8 - - + +
181B TRP* 3.7 27.1 - + - -
240B GSH 3.1 86.4 - - + +
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Residues in contact with SER 35 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B ILE* 4.2 0.6 - - - +
28B SER* 3.0 33.0 + - - -
29B MET 3.4 10.2 + - - -
32B CYS* 3.2 25.4 + - - +
34B TYR* 1.3 75.8 - - - +
36B HIS* 1.3 59.1 + - - +
38B THR* 3.2 3.5 + - - -
39B ARG* 2.9 33.7 + - - +
72B ILE* 4.3 2.2 - - - -
73B PRO* 3.8 27.5 - - - +
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Residues in contact with HIS 36 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32B CYS 3.1 16.1 + - - +
33B PRO* 3.3 12.6 - - + +
34B TYR 3.2 0.2 - - - -
35B SER* 1.3 73.1 + - - +
37B ARG* 1.3 64.5 + - - +
39B ARG* 3.2 30.7 + - - +
40B LEU* 3.0 39.1 + - + +
179B TRP* 4.1 12.3 - + - -
180B PRO* 3.6 8.8 - - + +
183B GLU* 3.2 33.0 + - - -
184B ARG* 3.2 22.6 + - - +
213B VAL 5.6 0.2 + - - -
216B LEU* 4.0 22.9 + - + +
218B MET* 5.2 4.2 - - + +
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Residues in contact with ARG 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 PRO 3.2 14.3 + - - +
34B TYR* 3.2 19.5 - - - +
36B HIS* 1.3 77.5 - - - +
38B THR* 1.3 64.0 + - - +
40B LEU* 3.3 10.0 + - - +
41B VAL* 3.2 22.5 + - - +
86B SER* 3.0 30.5 + - - -
87B VAL* 3.6 18.8 - - - +
90B CYS* 3.9 8.5 - - - -
117B LEU* 3.7 21.2 - - - +
120B PHE* 4.3 9.9 - - - -
124B PRO* 5.3 2.6 - - - +
176B TYR* 4.3 3.2 - - - +
177B LEU* 2.9 49.2 + - + +
180B PRO* 3.7 11.1 - - + +
181B TRP* 3.5 20.8 - - - -
240B GSH 3.7 7.7 + - - -
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Residues in contact with THR 38 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B ILE* 3.7 25.4 - - + -
34B TYR 3.7 0.2 + - - -
35B SER 3.2 4.1 + - - -
37B ARG* 1.3 73.4 - - - +
39B ARG* 1.3 61.1 + - - +
41B VAL* 3.2 2.8 + - - +
42B LEU* 3.0 28.5 + - + +
73B PRO* 3.5 20.7 - - + +
75B LEU* 4.2 5.2 - - + -
86B SER* 3.6 20.4 + - - -
89B ALA* 3.9 17.9 - - + -
90B CYS* 3.7 8.3 - - - -
93B LEU* 3.8 21.3 - - + -
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Residues in contact with ARG 39 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B ILE* 4.1 18.4 - - + -
28B SER* 3.5 24.5 + - - -
29B MET 4.9 1.2 + - - -
30B ARG* 3.7 24.9 + - - +
32B CYS 4.9 0.8 + - - -
35B SER* 2.9 20.2 + - - +
36B HIS* 3.7 32.6 - - - +
38B THR* 1.3 73.9 - - - +
40B LEU* 1.3 65.2 + - - +
42B LEU* 3.4 10.6 + - + +
43B LYS* 3.0 24.3 + - - +
49B HIS* 5.0 4.9 + - - +
51B VAL* 4.5 19.1 - - + -
53B ASN* 5.9 0.2 - - - -
184B ARG* 5.6 0.2 - - - +
216B LEU* 3.5 32.5 + - + +
218B MET* 5.9 3.0 - - - +
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Residues in contact with LEU 40 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36B HIS* 3.0 36.0 + - + +
37B ARG* 3.5 5.2 - - - +
38B THR 3.3 0.2 - - - -
39B ARG* 1.3 77.9 - - - +
41B VAL* 1.3 53.2 + - - +
43B LYS 3.3 0.5 + - - -
44B ALA* 2.7 39.3 + - - +
176B TYR* 3.6 41.5 - - + +
179B TRP* 4.0 21.1 - - + -
180B PRO* 4.2 5.4 - - + -
212B THR* 3.4 17.8 - - + +
213B VAL* 3.9 26.9 - - + +
216B LEU* 3.6 17.0 - - + -
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Residues in contact with VAL 41 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B ARG 3.2 4.7 + - - +
38B THR 3.2 8.3 + - - +
40B LEU* 1.3 76.7 - - - +
42B LEU* 1.3 62.7 + - - +
44B ALA* 3.8 0.6 - - - +
45B LYS* 3.1 31.8 + - + +
90B CYS* 3.6 35.0 - - - +
93B LEU* 3.8 30.5 - - + -
102B LEU* 4.0 20.4 - - + -
173B MET* 3.6 22.4 - - + -
176B TYR* 4.6 9.9 - - + -
177B LEU* 5.2 0.7 - - + -
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Residues in contact with LEU 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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24B ILE* 3.9 21.5 - - + -
26B ILE* 3.8 32.1 - - + -
38B THR 3.0 18.8 + - - +
39B ARG* 3.7 9.9 - - - +
41B VAL* 1.3 77.1 - - - +
43B LYS* 1.3 59.4 + - - +
45B LYS 3.5 0.3 + - - -
46B ASP 3.3 2.3 + - - -
47B ILE* 2.9 44.8 + - + +
49B HIS* 3.6 37.2 - - + +
75B LEU* 4.5 4.3 - - + -
93B LEU* 3.5 32.5 - - + -
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Residues in contact with LYS 43 (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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39B ARG 3.0 16.9 + - - +
42B LEU* 1.3 73.6 - - - +
44B ALA* 1.3 66.5 + - - +
46B ASP* 3.0 16.1 + - - +
48B ARG* 6.2 1.8 - - - +
49B HIS* 4.5 11.4 - - + -
212B THR* 3.8 27.5 + - + +
215B ALA* 4.2 19.1 - - - +
216B LEU* 3.9 19.5 - - + -
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Residues in contact with ALA 44 (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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40B LEU 2.7 22.7 + - - +
41B VAL 3.8 3.4 - - - +
43B LYS* 1.3 73.6 - - - +
45B LYS* 1.3 59.1 + - - +
46B ASP* 3.3 1.8 + - - +
100B ARG* 3.3 36.0 + - - +
102B LEU* 4.2 10.1 - - + -
176B TYR* 3.9 22.9 - - + +
212B THR* 3.3 19.8 + - - +
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Residues in contact with LYS 45 (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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41B VAL* 3.1 28.3 + - + +
44B ALA* 1.3 77.5 - - - +
46B ASP* 1.3 72.3 + - - +
47B ILE* 3.1 19.2 + - + +
93B LEU 3.5 15.9 - - - +
94B ASP* 3.0 32.9 + - - +
97B TYR* 3.1 31.3 + - - +
98B PRO 4.3 0.4 + - - -
99B GLY* 2.9 30.0 + - - +
100B ARG* 3.0 26.6 + - - +
101B LYS* 4.0 1.8 - - - +
102B LEU* 4.1 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
------------------------------------------------------------
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