Contacts of the helix formed by residues 33 - 48 (chain B) in PDB entry 5DTM
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 ALA 33 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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20B TYR* 4.1 16.2 - - + -
24B LEU* 4.1 7.2 - - + +
25B PRO* 3.0 39.8 + - + +
27B TYR* 3.5 24.9 - - - +
32B ASP* 1.4 70.2 - - - +
34B ALA* 1.3 58.4 + - - +
35B HIS 3.4 0.2 - - - -
36B GLU* 3.3 4.8 + - - +
37B ILE* 2.9 33.9 + - - +
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Residues in contact with ALA 34 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B LEU* 3.7 26.9 - - + +
32B ASP* 3.0 13.5 + - - +
33B ALA* 1.3 74.6 - - - +
35B HIS* 1.4 65.5 + - - +
37B ILE* 3.3 4.6 + - - +
38B ILE* 3.1 29.7 + - - +
65B THR* 3.7 33.0 - - + +
71B MET* 3.9 9.6 - - + +
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Residues in contact with HIS 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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128A TYR 5.8 0.8 + - - -
130A PRO* 3.8 38.9 - - + +
30B HIS 4.0 15.7 + - - -
31B HIS* 4.1 4.5 - + + -
32B ASP* 3.1 45.8 + - - +
34B ALA* 1.4 75.8 - - - +
36B GLU* 1.3 57.3 + - - +
38B ILE* 3.4 8.9 + - - +
39B GLU* 3.0 49.9 + - - +
63B TYR* 5.6 2.8 + + - -
65B THR* 4.3 22.1 - - + +
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Residues in contact with GLU 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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20B TYR* 2.7 25.5 + - - -
27B TYR* 2.7 31.9 + - + -
32B ASP 3.3 7.7 + - - +
33B ALA* 3.4 12.1 - - - +
34B ALA 3.2 0.2 - - - -
35B HIS* 1.3 78.5 - - - +
37B ILE* 1.3 53.7 + - - +
39B GLU* 3.5 6.3 + - - -
40B THR* 2.7 38.9 + - - +
109B HIS* 3.9 8.0 - - + -
113B GLN* 2.9 32.6 + - + +
116B ASN* 4.3 2.2 + - - +
117B HIS* 2.8 27.6 + - - -
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Residues in contact with ILE 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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7B LEU* 3.8 30.1 - - + -
9B LEU* 4.2 11.2 - - + +
20B TYR* 3.8 36.1 - - + -
24B LEU* 3.8 19.5 - - + -
33B ALA 2.9 18.3 + - - +
34B ALA 3.3 7.2 + - - +
36B GLU* 1.3 75.5 - - - +
38B ILE* 1.3 63.3 + - - +
40B THR* 3.4 2.5 + - - -
41B ILE* 3.0 37.2 + - + +
71B MET* 4.0 11.7 - - + -
74B LEU* 4.4 1.8 - - + -
75B CYS* 3.7 24.2 - - - -
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Residues in contact with ILE 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 ALA 3.1 24.2 + - - +
35B HIS* 3.8 9.2 - - - +
37B ILE* 1.3 74.8 - - - +
39B GLU* 1.3 61.5 + - + +
41B ILE* 3.4 8.1 + - - +
42B ARG* 3.0 65.6 + - - +
60B LEU* 4.2 7.9 - - + +
63B TYR* 3.3 46.2 - - + +
65B THR* 3.9 11.9 - - + -
71B MET* 4.3 6.1 - - + -
74B LEU* 3.6 21.8 - - + -
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Residues in contact with GLU 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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308A LYS* 3.1 49.0 + - - +
309A PRO* 3.7 26.6 - - + +
310A VAL* 5.6 3.2 - - + +
35B HIS* 3.0 34.7 + - - +
36B GLU* 4.5 2.0 - - - -
38B ILE* 1.3 79.5 - - + +
40B THR* 1.3 58.6 + - - +
42B ARG* 4.3 3.8 - - - +
43B TRP* 2.9 34.5 + - - +
109B HIS* 3.9 22.3 + - + +
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Residues in contact with THR 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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9B LEU* 4.1 13.9 - - + -
20B TYR* 4.5 0.7 + - - +
36B GLU 2.7 27.3 + - - -
37B ILE* 3.6 5.8 - - - -
39B GLU* 1.3 70.5 - - - +
41B ILE* 1.3 64.3 + - - +
43B TRP* 3.2 3.6 + - - +
44B VAL* 3.0 27.5 + - - +
109B HIS* 2.9 21.8 + - - -
113B GLN* 3.2 15.3 + - - +
205B TRP* 4.8 2.5 - - + -
208B TRP* 3.6 32.1 - - + -
209B TYR* 3.4 16.4 - - + +
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Residues in contact with ILE 41 (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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9B LEU* 3.8 20.2 - - + -
37B ILE* 3.0 39.6 + - + +
38B ILE* 3.7 4.3 - - - +
39B GLU 3.3 0.2 - - - -
40B THR* 1.3 75.8 - - - +
42B ARG* 1.3 62.4 + - - +
44B VAL* 3.3 1.6 + - - +
45B CYS* 3.0 25.2 + - - -
55B MET* 4.1 18.4 - - + -
60B LEU* 4.1 15.0 - - + -
74B LEU* 3.9 26.2 - - + +
75B CYS* 4.6 0.7 - - - -
78B TYR* 3.7 46.9 - - + -
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Residues in contact with ARG 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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309A PRO* 3.2 41.5 + - + +
310A VAL* 4.5 10.9 - - - +
311A SER* 5.2 4.4 - - - +
313A TYR* 5.9 1.2 + - - -
401A 5F4 4.8 10.9 + - - -
38B ILE* 3.0 37.9 + - - +
39B GLU* 3.7 8.7 - - - +
40B THR 3.3 0.2 - - - -
41B ILE* 1.3 75.1 - - - +
43B TRP* 1.3 57.5 + - - +
45B CYS* 3.4 6.7 + - - +
46B GLU* 2.9 31.2 + - - +
52B LYS* 5.7 0.3 - - - -
60B LEU* 2.9 50.0 + - + +
63B TYR* 3.8 18.2 + - - -
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Residues in contact with TRP 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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299A LEU* 3.6 34.5 - - + -
305A TRP 5.2 1.1 - - - -
307A GLY 3.6 20.7 + - - -
308A LYS* 5.0 0.6 - - - +
309A PRO* 3.5 24.3 - - + +
39B GLU 2.9 23.4 + - - +
40B THR* 3.2 6.0 + - - +
42B ARG* 1.3 76.9 - - - +
44B VAL* 1.4 62.2 + - + +
46B GLU* 3.4 12.4 + - + +
47B GLU* 3.1 57.4 + - + +
103B SER* 4.3 1.1 - - - -
105B GLY* 3.4 34.0 + - - -
106B LEU* 3.8 24.9 - - + -
109B HIS* 3.6 33.1 - + + +
209B TYR* 5.2 0.4 - - + -
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Residues in contact with VAL 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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12B PRO* 3.8 24.0 - - + -
40B THR 3.0 17.6 + - - +
41B ILE 3.9 3.4 - - - +
43B TRP* 1.4 72.8 - - - +
45B CYS* 1.4 56.7 + - - +
47B GLU* 3.4 2.6 + - - -
48B ILE* 2.9 36.1 + - + +
51B LEU* 3.4 21.8 - - + -
78B TYR* 3.8 19.5 - - + +
208B TRP* 3.9 28.3 - - + -
209B TYR* 4.0 14.6 - - + -
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Residues in contact with CYS 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 ILE* 3.0 25.7 + - - +
42B ARG* 3.7 6.7 - - - +
44B VAL* 1.4 72.6 - - - +
46B GLU* 1.3 64.0 + - - +
48B ILE 3.1 20.6 + - - +
49B PRO* 4.2 0.9 - - - +
51B LEU* 3.9 23.8 - - - -
52B LYS* 3.5 36.5 - - + +
55B MET* 4.0 27.8 - - - -
57B ASN* 5.7 1.1 - - - -
60B LEU* 5.0 6.3 - - + -
78B TYR* 4.8 0.4 - - - -
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Residues in contact with GLU 46 (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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299A LEU* 3.8 52.6 - - + +
300A LYS* 5.2 3.5 + - - +
42B ARG 2.9 18.1 + - - +
43B TRP* 3.6 20.2 - - + +
45B CYS* 1.3 77.0 - - - +
47B GLU* 1.3 63.4 + - + +
49B PRO* 4.9 6.4 - - - +
52B LYS* 2.8 33.5 + - - +
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Residues in contact with GLU 47 (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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43B TRP* 3.1 39.1 + - + +
44B VAL* 4.3 2.5 - - - +
46B GLU* 1.3 84.7 - - + +
48B ILE* 1.4 65.0 + - + +
49B PRO* 3.4 10.6 - - - +
103B SER* 2.8 32.9 + - - -
106B LEU* 3.4 25.2 - - - +
211B LYS* 4.3 12.5 + - - +
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Residues in contact with ILE 48 (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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12B PRO* 3.5 32.3 - - + -
13B VAL* 6.2 0.9 - - + -
44B VAL* 2.9 25.1 + - + +
45B CYS 3.1 12.7 - - - +
47B GLU* 1.4 83.8 - - + +
49B PRO* 1.4 69.0 - - + +
50B ASP* 4.3 4.3 - - + +
51B LEU* 3.0 33.0 + - + +
52B LYS 3.2 4.0 + - - -
82B ILE* 5.7 0.4 - - + -
85B ILE* 5.1 2.5 - - + -
89B TRP* 3.7 37.7 - - + -
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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