Contacts of the helix formed by residues 41 - 59 (chain B) in PDB entry 3ISL
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 41 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14A ARG* 2.7 52.6 + - - +
345A LEU* 3.9 13.0 - - + +
351A GLU* 4.5 9.6 + - - +
37B VAL* 3.9 13.0 - - + +
38B GLY* 3.3 24.9 + - - +
40B PHE* 1.3 79.1 - - - +
42B PRO* 1.4 60.1 - - - +
43B ALA* 2.9 23.7 + - - +
44B PHE* 2.7 25.1 + - - +
45B THR* 3.1 9.6 + - - -
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Residues in contact with PRO 42 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A ARG* 4.4 4.5 - - - +
345A LEU* 3.5 20.4 - - + -
40B PHE 3.5 4.9 - - - +
41B ASP* 1.4 90.5 - - - +
43B ALA* 1.3 62.1 + - - +
45B THR* 3.0 11.8 + - - +
46B GLY* 3.0 21.1 + - - -
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Residues in contact with ALA 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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10A CYS 5.8 0.9 - - - +
11A THR* 4.4 9.9 - - - +
12A PRO* 3.7 30.7 - - + -
14A ARG* 4.9 1.7 - - - +
37B VAL* 4.5 4.7 - - + -
41B ASP* 2.9 16.7 + - - +
42B PRO* 1.3 78.2 - - - +
44B PHE* 1.3 61.7 + - - +
46B GLY* 3.5 1.8 + - - -
47B ILE* 3.1 28.7 + - + +
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Residues in contact with PHE 44 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B VAL* 3.6 22.5 - - + +
38B GLY 3.1 22.7 - - - +
39B GLN* 3.6 25.1 - - - +
41B ASP 2.7 14.2 + - - +
43B ALA* 1.3 73.4 - - - +
45B THR* 1.3 58.7 + - - +
47B ILE* 3.1 11.4 + - + +
48B MET* 2.9 41.0 + - - +
270B GLU* 4.0 27.6 - - + -
272B THR* 3.8 41.5 - - + -
275B LEU* 3.6 28.0 - - + -
276B TYR* 4.5 8.3 - + - -
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Residues in contact with THR 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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39B GLN 4.1 14.4 - - - +
40B PHE* 4.7 7.4 - - - +
41B ASP 3.1 10.0 + - - +
42B PRO* 3.0 24.6 + - - +
44B PHE* 1.3 77.1 - - - +
46B GLY* 1.3 53.8 + - - +
48B MET* 3.2 10.8 + - - +
49B ASN* 2.9 38.2 + - - -
264B ARG* 3.6 38.4 - - + +
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Residues in contact with GLY 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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42B PRO 3.0 16.0 + - - -
43B ALA* 3.9 1.8 - - - -
45B THR* 1.3 72.9 + - - +
47B ILE* 1.3 66.2 + - - +
49B ASN* 3.4 7.9 + - - +
50B GLU* 3.1 26.5 + - - +
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Residues in contact with ILE 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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9A LEU* 3.9 22.0 - - + -
10A CYS 5.7 1.8 - - - +
11A THR* 4.0 12.6 - - - +
37B VAL* 4.9 0.7 - - + -
43B ALA* 3.1 19.5 + - + +
44B PHE* 3.1 13.3 + - + +
46B GLY* 1.3 76.1 - - - +
48B MET* 1.3 56.2 + - - +
50B GLU* 3.3 6.4 + - - +
51B THR* 2.8 36.4 + - - -
275B LEU* 3.7 28.7 - - + +
276B TYR* 3.6 30.5 - - + -
279B ARG* 3.9 25.7 - - + +
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Residues in contact with MET 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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39B GLN 4.6 7.6 - - - +
44B PHE* 2.9 36.7 + - + +
45B THR* 3.2 15.5 + - - +
47B ILE* 1.3 76.7 - - - +
49B ASN* 1.3 67.2 + - - +
51B THR* 3.4 2.3 + - - -
52B MET* 3.0 29.3 + - - +
259B TYR* 3.7 30.3 - - + +
260B TRP* 3.4 51.8 - - + -
264B ARG* 3.4 33.2 - - - +
275B LEU* 3.8 13.7 - - + -
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Residues in contact with ASN 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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45B THR* 2.9 22.9 + - - +
46B GLY* 3.8 7.1 - - - +
48B MET* 1.3 77.8 - - - +
50B GLU* 1.3 59.8 + - - +
52B MET* 3.3 15.6 + - - +
53B GLU* 3.3 25.3 + - - +
56B ARG* 5.0 0.5 + - - -
264B ARG* 2.8 27.4 + - - +
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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
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7A ARG* 3.1 32.5 + - - +
46B GLY 3.1 17.5 + - - +
47B ILE* 3.8 4.5 - - - +
49B ASN* 1.3 72.9 - - - +
51B THR* 1.3 61.6 + - - +
53B GLU* 3.2 20.6 + - - +
54B MET* 2.9 43.1 + - + +
279B ARG* 3.0 31.1 + - - +
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Residues in contact with THR 51 (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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47B ILE* 2.8 24.5 + - - +
48B MET 3.7 4.0 - - - -
50B GLU* 1.3 77.9 - - - +
52B MET* 1.3 61.9 + - - +
54B MET* 3.3 10.7 + - + +
55B LEU* 2.9 38.8 + - + +
68B PRO* 4.8 3.4 - - + -
260B TRP* 5.2 1.3 - - - -
275B LEU* 4.0 15.3 - - + +
278B LEU* 4.0 31.9 - - + -
279B ARG* 3.3 27.1 - - - +
282B VAL* 5.5 1.8 - - + -
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Residues in contact with MET 52 (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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48B MET 3.0 20.0 + - - +
49B ASN* 3.7 17.9 - - - +
50B GLU 3.2 0.2 - - - -
51B THR* 1.3 75.8 - - - +
53B GLU* 1.3 61.5 + - - +
55B LEU* 3.3 5.3 + - - +
56B ARG* 3.1 42.3 + - - +
64B ARG 4.0 19.7 - - - +
65B TRP* 4.8 1.8 - - + -
66B ALA* 3.1 29.8 - - - +
67B TYR* 4.1 19.1 - - + -
68B PRO* 5.4 0.2 - - + -
260B TRP* 3.5 50.9 - - + +
261B SER* 5.9 0.2 - - - -
264B ARG* 5.7 0.4 - - - -
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Residues in contact with GLU 53 (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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49B ASN 3.3 14.1 + - - +
50B GLU* 3.2 23.1 + - - +
52B MET* 1.3 73.5 - - - +
54B MET* 1.3 68.2 + - + +
56B ARG* 3.4 24.8 + - - +
57B GLU* 3.3 24.9 + - - +
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Residues in contact with MET 54 (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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7A ARG* 4.1 23.1 - - - +
50B GLU* 2.9 27.3 + - + +
51B THR* 3.8 8.3 - - + +
53B GLU* 1.3 78.9 - - + +
55B LEU* 1.3 57.0 + - - +
57B GLU* 3.3 6.8 + - - +
58B LEU* 2.8 29.3 + - - +
279B ARG* 3.3 49.1 - - + +
282B VAL* 3.6 16.6 - - + -
283B ARG* 3.6 31.4 - - + +
286B LEU* 3.8 20.2 - - + +
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Residues in contact with LEU 55 (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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51B THR* 2.9 29.5 + - + +
52B MET 3.3 5.1 + - - +
53B GLU 3.2 0.2 - - - -
54B MET* 1.3 74.3 - - - +
56B ARG* 1.3 58.7 + - - +
58B LEU* 3.8 26.0 - - + -
59B PHE* 2.9 43.3 + - + -
66B ALA* 3.9 11.9 - - + +
67B TYR* 3.8 32.1 - - - +
68B PRO* 4.0 12.6 - - + -
210B PRO* 3.9 24.7 - - + -
211B ILE 5.1 0.4 - - - +
278B LEU* 4.7 4.3 - - + -
282B VAL* 4.1 16.6 - - + -
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Residues in contact with ARG 56 (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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49B ASN 5.0 0.4 + - - -
52B MET* 3.1 36.2 + - - +
53B GLU* 3.6 38.4 - - - +
54B MET 3.3 0.2 - - - -
55B LEU* 1.3 76.3 - - - +
57B GLU* 1.4 60.4 + - + +
60B GLN 3.1 3.1 + - - -
61B THR* 2.9 49.8 + - + +
62B LYS* 4.7 5.4 - - - +
63B ASN 2.9 26.7 + - - +
64B ARG* 2.8 30.8 + - - +
66B ALA* 3.9 9.0 - - + +
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Residues in contact with GLU 57 (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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53B GLU* 3.3 13.6 + - - +
54B MET* 3.3 8.6 + - - +
56B ARG* 1.4 74.1 - - + +
58B LEU* 1.3 68.1 + - - +
60B GLN* 3.1 13.1 + - - +
286B LEU* 3.8 32.4 - - + +
290B LEU* 3.5 16.3 - - + +
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Residues in contact with LEU 58 (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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54B MET 2.8 17.3 + - - +
55B LEU* 3.6 29.2 - - + +
56B ARG 3.3 0.2 - - - -
57B GLU* 1.3 79.7 - - - +
59B PHE* 1.3 62.8 + - + +
60B GLN* 3.4 6.4 + - - +
179B ILE* 3.8 35.7 - - + +
180B GLY* 4.3 8.1 - - - +
184B VAL* 4.4 2.9 - - - +
202B LEU* 4.0 27.4 - - + -
210B PRO* 5.4 0.9 - - + -
282B VAL* 4.3 12.6 - - + -
285B VAL* 3.9 26.9 - - + -
286B LEU* 4.4 6.7 - - + +
290B LEU* 4.2 9.8 - - + +
294B PHE* 5.9 1.0 - - - -
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Residues in contact with PHE 59 (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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55B LEU* 2.9 37.5 + - + +
58B LEU* 1.3 77.7 - - + +
60B GLN* 1.3 66.8 + - - +
61B THR* 3.4 7.0 - - + -
175B ALA* 5.1 2.2 - - + -
179B ILE* 3.7 29.8 - - + -
184B VAL* 3.6 5.9 - - + +
186B VAL* 3.2 40.9 + - + +
194B ALA* 4.0 20.6 - - + -
195B ILE 4.5 1.3 - - - -
196B GLY* 3.9 13.0 - - - -
210B PRO* 3.4 39.5 - - + -
211B ILE 4.0 9.6 - - - -
212B THR* 3.4 28.9 - - + -
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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
------------------------------------------------------------
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