Contacts of the helix formed by residues 34 - 52 (chain B) in PDB entry 3ROT
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 ASP 34 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32B SER 3.5 2.5 - - - +
33B GLN* 1.3 81.5 - - - +
35B PRO* 1.3 72.8 - - - +
36B TYR* 3.0 28.7 + - + +
37B TRP* 3.2 32.8 + - + +
38B THR* 3.5 10.2 + - - +
215B THR* 5.9 0.7 - - - -
216B SER* 2.9 30.3 + - - -
217B GLN* 3.4 32.4 + - + +
244B ASP* 5.0 1.9 - - - +
246B THR* 4.1 1.0 - - - +
317B GOL 5.8 1.0 - - - -
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Residues in contact with PRO 35 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191A PRO* 6.3 0.2 - - + -
220A ASP* 6.3 2.7 - - + -
224A GLN* 3.0 24.7 + - - +
33B GLN 4.1 2.7 - - - +
34B ASP* 1.3 98.1 - - - +
36B TYR* 1.3 59.4 + - - +
38B THR* 2.8 22.1 + - + +
39B SER* 3.2 8.1 + - - -
216B SER* 4.6 1.1 - - - +
220B ASP* 5.7 6.1 - - - +
246B THR* 3.9 16.2 - - + -
247B PRO* 3.9 20.2 - - + -
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Residues in contact with TYR 36 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34B ASP* 3.2 21.1 + - + +
35B PRO* 1.3 80.0 - - - +
37B TRP* 1.3 89.4 + + - +
39B SER* 3.4 7.9 + - - -
40B LEU* 3.2 23.7 + - + +
112B ASP* 2.7 28.4 + - - -
244B ASP* 3.4 26.9 - - + +
246B THR* 4.3 6.3 - - + +
264B GLN* 3.3 25.9 + - - -
266B PRO* 3.6 37.4 - - + +
269B MSE 3.4 22.5 - - - +
317B GOL 3.6 13.0 - - - -
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Residues in contact with TRP 37 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29B THR* 3.7 25.6 - - + -
30B HIS* 3.6 42.2 - + - -
31B GLY* 3.3 24.0 - - - -
32B SER* 3.5 30.3 - - - +
33B GLN 4.1 0.2 - - - -
34B ASP* 3.2 34.4 + - + +
36B TYR* 1.3 85.2 - + - +
38B THR* 1.3 59.2 + - - +
40B LEU* 3.1 28.0 + - + +
41B PHE* 2.7 43.2 + + + -
63B ALA* 5.1 3.0 + - - +
87B THR* 4.0 7.0 - - + -
112B ASP* 3.9 13.0 - - - -
217B GLN* 5.4 5.3 - - - +
317B GOL 3.8 13.5 - - - -
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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
----------------------------------------------------------
191A PRO* 3.3 35.4 - - + +
192A ASN* 3.9 14.1 - - + +
195A GLN* 4.1 12.8 - - - +
221A PRO* 5.7 0.2 - - + -
224A GLN* 2.6 26.9 + - - +
232A TYR* 3.6 3.9 + - - -
32B SER 4.6 4.5 - - - +
34B ASP 3.5 5.3 + - - +
35B PRO* 2.8 20.3 + - - +
37B TRP* 1.3 76.3 - - - +
39B SER* 1.3 60.1 + - - +
41B PHE* 3.7 10.2 - - + +
42B GLN* 3.0 25.5 + - - +
45B LYS* 5.9 0.2 + - - -
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Residues in contact with SER 39 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224A GLN* 3.4 11.8 + - - -
231A ARG* 5.2 7.2 + - - -
232A TYR* 3.5 12.4 + - - -
35B PRO 3.2 14.5 + - - -
36B TYR* 3.6 8.6 - - - -
37B TRP 3.2 0.2 - - - -
38B THR* 1.3 75.6 + - - +
40B LEU* 1.3 63.2 + - - +
42B GLN* 3.2 3.9 + - - +
43B GLY 3.1 18.9 + - - -
266B PRO* 3.7 19.0 - - - +
267B PHE* 3.5 19.8 - - - -
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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
----------------------------------------------------------
27B LEU* 3.6 33.0 - - + -
29B THR* 5.0 1.6 - - + -
36B TYR* 3.2 17.7 + - + +
37B TRP* 3.1 34.9 + - + +
39B SER* 1.3 80.3 - - - +
41B PHE* 1.3 66.8 + - + +
43B GLY 3.4 1.0 + - - -
44B ALA* 3.3 18.2 + - - +
111B VAL* 5.0 8.5 - - + -
112B ASP* 4.8 4.9 - - + -
266B PRO* 3.4 25.0 - - + +
269B MSE 4.1 22.7 - - + -
270B GLY* 3.6 14.9 - - - +
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Residues in contact with PHE 41 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192A ASN* 4.0 34.5 - - + +
27B LEU* 3.9 15.9 - - + -
29B THR* 3.8 35.2 - - + -
31B GLY 3.9 2.7 - - - -
32B SER* 3.8 31.6 - - - -
37B TRP* 2.7 38.1 + + + +
38B THR* 3.7 9.2 - - + +
39B SER 3.2 0.2 - - - -
40B LEU* 1.3 74.3 - - + +
42B GLN* 1.3 58.2 + - - +
44B ALA* 3.4 3.3 + - - +
45B LYS* 2.9 34.1 + - - +
57B ILE* 3.8 36.4 - - + +
59B ALA* 4.0 2.7 - - + -
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Residues in contact with GLN 42 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195A GLN* 5.5 0.2 - - - +
199A LYS* 3.7 17.9 + - - +
231A ARG 2.9 29.5 + - - +
232A TYR* 3.4 42.4 - - + +
233A ASP* 4.5 1.4 + - - -
38B THR 3.0 18.2 + - - +
39B SER 3.6 4.0 - - - +
41B PHE* 1.3 76.0 - - - +
43B GLY* 1.3 61.0 + - - +
45B LYS* 3.2 28.0 + - - +
46B LYS* 2.8 44.5 + - - +
267B PHE* 3.8 7.6 - - + -
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Residues in contact with GLY 43 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39B SER 3.1 10.7 + - - -
40B LEU 3.4 2.4 + - - -
41B PHE 3.3 0.4 - - - -
42B GLN* 1.3 75.2 - - - +
44B ALA* 1.3 57.0 + - - +
46B LYS* 3.3 3.3 + - - +
47B ALA 3.0 23.6 + - - -
267B PHE* 3.5 40.8 - - - -
271B TYR* 3.3 17.3 - - - -
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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
----------------------------------------------------------
27B LEU* 3.6 31.2 - - + -
40B LEU 3.3 6.4 + - - +
41B PHE 3.6 4.3 - - - +
43B GLY* 1.3 74.8 - - - +
45B LYS* 1.3 59.7 + - - +
47B ALA* 3.3 2.4 + - - +
48B ALA* 2.9 30.0 + - - +
55B LEU* 3.5 14.9 - - + +
270B GLY* 3.4 16.6 - - - +
271B TYR* 4.4 0.4 - - - +
273B SER* 5.2 0.2 - - - +
274B ILE* 3.7 17.6 - - + +
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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
----------------------------------------------------------
192A ASN* 2.8 29.1 + - - +
195A GLN* 4.6 10.7 + - - +
196A SER* 4.2 12.8 + - - +
199A LYS* 5.2 4.9 - - - +
38B THR 5.9 0.2 + - - -
41B PHE* 2.9 24.9 + - - +
42B GLN* 3.2 31.8 + - - +
43B GLY 3.3 0.2 - - - -
44B ALA* 1.3 76.0 - - - +
46B LYS* 1.3 57.0 + - - +
48B ALA* 3.5 3.6 + - - +
49B GLU* 3.0 32.0 + - - +
55B LEU* 3.9 10.5 - - + +
57B ILE* 3.9 18.8 - - + -
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Residues in contact with LYS 46 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230A ASP 3.8 8.9 + - - -
231A ARG* 3.8 19.5 - - - +
233A ASP* 3.0 39.9 + - - +
42B GLN* 2.8 22.6 + - - +
43B GLY 3.4 5.4 - - - +
45B LYS* 1.3 74.3 - - - +
47B ALA* 1.3 65.8 + - - +
49B GLU* 3.4 11.1 + - - +
50B GLU* 3.1 48.1 + - - +
267B PHE* 4.2 13.2 - - + -
271B TYR* 4.0 16.8 - - + -
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Residues in contact with ALA 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 GLY 3.0 14.9 + - - +
44B ALA 3.7 3.8 - - - +
46B LYS* 1.3 73.3 - - - +
48B ALA* 1.3 67.5 + - - +
50B GLU* 3.1 2.1 + - - -
51B LEU* 2.9 32.1 + - + +
271B TYR* 3.4 43.7 - - + +
274B ILE* 3.9 11.9 - - + -
275B THR* 3.8 10.8 - - - +
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Residues in contact with ALA 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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22B ARG* 5.5 0.2 + - - -
44B ALA 2.9 17.9 + - - +
45B LYS* 3.6 6.1 - - - +
47B ALA* 1.3 75.8 - - - +
49B GLU* 1.3 57.6 - - - +
51B LEU 3.7 0.3 - - - -
52B LYS* 2.9 24.8 + - - -
53B VAL* 3.0 40.2 + - + +
55B LEU* 3.7 25.1 - - + +
274B ILE* 4.1 5.3 - - + +
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Residues in contact with GLU 49 (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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233A ASP* 4.4 16.1 - - - +
22B ARG* 6.1 1.1 - - - +
45B LYS 3.0 18.8 + - - +
46B LYS* 3.7 11.6 - - - +
47B ALA 3.2 0.2 - - - -
48B ALA* 1.3 77.8 - - - +
50B GLU* 1.3 66.4 + - + +
52B LYS* 3.4 18.0 + - - +
53B VAL 5.2 0.4 - - - -
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Residues in contact with GLU 50 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46B LYS* 3.1 38.3 + - + +
47B ALA 3.1 2.7 + - - +
49B GLU* 1.3 80.7 - - + +
51B LEU* 1.3 63.9 + - + +
52B LYS* 3.7 16.3 + - - +
271B TYR* 3.5 29.6 + - - +
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Residues in contact with LEU 51 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47B ALA* 2.9 23.4 + - + +
48B ALA 4.2 2.0 - - - +
50B GLU* 1.3 81.1 - - + +
52B LYS* 1.3 72.2 + - - +
53B VAL* 3.8 3.6 - - + +
271B TYR* 5.9 2.0 - - + +
274B ILE* 4.3 0.9 - - + +
275B THR* 3.8 33.7 - - + +
278B VAL* 3.6 40.4 - - + -
279B LEU* 5.6 4.7 - - + -
282B ARG* 3.0 42.4 + - - +
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Residues in contact with LYS 52 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B ARG* 3.6 37.3 + - - +
23B ASP 5.6 0.5 + - - -
48B ALA 2.9 8.4 + - - -
49B GLU 3.4 12.4 + - - +
50B GLU* 3.3 14.5 + - - +
51B LEU* 1.3 83.6 - - - +
53B VAL* 1.3 59.9 + - - +
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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
------------------------------------------------------------
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