Contacts of the helix formed by residues 41 - 59 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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37A VAL* 4.0 4.7 - - + +
38A GLY* 3.2 25.2 + - - +
40A PHE* 1.3 79.0 - - - +
42A PRO* 1.3 61.0 - - - +
43A ALA* 2.8 33.2 + - - +
44A PHE* 2.6 26.8 + - - +
45A THR* 3.1 9.9 + - - -
14B ARG* 2.7 52.2 + - - +
345B LEU* 3.9 13.5 - - + +
351B GLU* 4.7 7.5 + - - +
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Residues in contact with PRO 42 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40A PHE 3.7 5.6 - - - +
41A ASP* 1.3 87.9 - - - +
43A ALA* 1.3 62.4 + - - +
45A THR* 3.1 13.4 + - + +
46A GLY* 2.9 21.7 + - - -
14B ARG* 4.7 3.4 - - - +
345B LEU* 3.7 18.4 - - + -
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Residues in contact with ALA 43 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37A VAL* 4.4 9.0 - - + -
41A ASP* 2.8 23.7 + - - +
42A PRO* 1.3 73.0 - - - +
44A PHE* 1.3 60.7 + - - +
46A GLY* 3.6 1.0 + - - -
47A ILE* 3.2 28.6 + - - +
10B CYS 6.1 0.2 - - - +
11B THR* 5.0 3.6 - - + -
12B PRO* 3.7 33.2 - - + -
14B ARG* 4.4 1.7 - - - +
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Residues in contact with PHE 44 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A VAL* 3.7 20.6 - - + +
38A GLY 3.0 22.0 - - - +
39A GLN* 3.6 15.0 - - - +
41A ASP 2.6 13.2 + - - +
43A ALA* 1.3 71.5 - - - +
45A THR* 1.3 59.3 + - - +
46A GLY 3.1 1.8 - - - -
47A ILE* 3.1 10.7 + - + +
48A MET* 2.6 70.1 + - + +
270A GLU* 3.5 25.4 - - + -
272A THR* 3.6 42.4 - - + -
275A LEU* 3.2 28.0 - - + -
276A TYR* 4.7 2.9 - + - -
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Residues in contact with THR 45 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39A GLN 4.0 16.8 - - - +
40A PHE* 5.0 4.7 - - - -
41A ASP 3.1 8.9 + - - +
42A PRO* 3.1 23.6 + - - +
44A PHE* 1.3 73.5 - - - +
46A GLY* 1.3 54.4 + - - +
48A MET* 3.1 10.6 + - - +
49A ASN* 2.9 37.6 + - - -
264A ARG* 3.5 40.2 - - + +
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Residues in contact with GLY 46 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42A PRO 2.9 16.4 + - - -
43A ALA 3.9 1.8 - - - -
45A THR* 1.3 73.8 + - - +
47A ILE* 1.3 63.2 + - - +
49A ASN* 3.4 7.7 + - - +
50A GLU* 3.1 26.8 + - - +
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Residues in contact with ILE 47 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37A VAL* 4.9 1.1 - - + -
43A ALA 3.2 19.5 + - - +
44A PHE* 3.1 12.0 + - + +
46A GLY* 1.3 73.5 - - - +
48A MET* 1.4 65.1 + - - +
50A GLU* 3.5 6.7 + - - +
51A THR* 3.0 28.7 + - - +
275A LEU* 3.5 31.2 - - + +
276A TYR* 3.6 30.5 - - + -
279A ARG* 3.9 24.9 - - + +
9B LEU* 3.8 15.7 - - + -
10B CYS 5.9 0.9 - - - +
11B THR* 3.7 20.2 - - + -
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Residues in contact with MET 48 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39A GLN* 3.7 13.2 - - - +
44A PHE* 2.6 67.8 + - + +
45A THR* 3.1 16.3 + - - +
47A ILE* 1.4 72.5 - - - +
49A ASN* 1.3 67.3 + - - +
51A THR* 3.1 5.0 + - - -
52A MET* 3.0 27.6 + - - +
259A TYR* 4.2 18.4 - - + +
260A TRP* 3.2 35.7 - - + -
264A ARG* 3.9 21.8 - - - +
270A GLU* 4.1 12.3 - - + -
275A LEU* 3.9 7.2 - - + -
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Residues in contact with ASN 49 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45A THR* 2.9 22.6 + - - +
46A GLY* 4.0 6.4 - - - +
47A ILE 3.3 0.2 - - - -
48A MET* 1.3 77.7 - - - +
50A GLU* 1.3 61.6 + - - +
52A MET* 3.5 18.2 + - - +
53A GLU* 3.3 24.5 + - - +
56A ARG* 5.0 0.5 + - - -
261A SER* 5.9 0.3 - - - -
264A ARG* 2.9 28.7 + - - +
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Residues in contact with GLU 50 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46A GLY 3.1 16.9 + - - +
47A ILE* 4.0 5.7 - - - +
49A ASN* 1.3 75.5 - - - +
51A THR* 1.3 66.4 + - - +
53A GLU* 3.4 9.3 + - + +
54A MET* 3.0 37.3 + - + +
279A ARG* 2.9 30.3 + - - +
7B ARG* 2.4 31.5 + - - +
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Residues in contact with THR 51 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47A ILE* 3.0 24.8 + - - +
48A MET* 3.5 4.9 - - - -
50A GLU* 1.3 78.5 - - - +
52A MET* 1.3 56.7 + - - +
54A MET* 3.2 10.8 + - + +
55A LEU* 2.9 40.6 + - + +
68A PRO* 4.7 4.3 - - + -
260A TRP* 5.1 1.1 - - - -
275A LEU* 4.1 12.6 - - + +
278A LEU* 4.0 32.1 - - + -
279A ARG* 3.5 26.4 - - - +
282A VAL* 5.5 2.0 - - + -
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Residues in contact with MET 52 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48A MET* 3.0 15.8 + - + +
49A ASN* 3.8 24.9 - - - +
50A GLU 3.3 0.2 - - - -
51A THR* 1.3 73.6 - - - +
53A GLU* 1.3 64.8 + - - +
55A LEU* 3.2 4.9 + - - +
56A ARG* 3.0 46.0 + - - +
64A ARG 5.3 2.2 - - - +
66A ALA 3.2 26.1 - - - +
67A TYR* 4.0 6.3 - - + -
260A TRP* 2.8 74.3 - - + +
261A SER* 5.0 0.7 - - - -
264A ARG* 4.3 2.7 - - - +
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Residues in contact with GLU 53 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49A ASN 3.3 13.6 + - - +
50A GLU* 3.7 10.8 - - + +
51A THR 3.4 0.2 - - - -
52A MET* 1.3 78.2 - - - +
54A MET* 1.3 63.6 + - + +
56A ARG* 3.1 45.3 + - - +
57A GLU* 3.4 17.3 + - - +
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Residues in contact with MET 54 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50A GLU* 3.0 31.7 + - + +
51A THR* 3.2 7.6 + - + +
53A GLU* 1.3 78.1 - - + +
55A LEU* 1.3 59.0 + - - +
57A GLU* 3.2 9.8 + - - +
58A LEU* 2.9 27.4 + - - +
279A ARG* 3.4 51.6 - - + +
282A VAL* 3.9 12.1 - - + +
283A ARG* 3.7 30.5 - - + +
286A LEU* 3.7 23.7 - - + +
7B ARG* 5.4 7.4 - - - -
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Residues in contact with LEU 55 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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51A THR* 2.9 29.4 + - + +
52A MET 3.2 4.5 + - - +
54A MET* 1.3 74.1 - - - +
56A ARG* 1.3 65.0 + - - +
58A LEU* 4.1 14.6 - - + -
59A PHE* 3.0 34.0 + - + -
66A ALA* 3.9 12.6 - - + +
67A TYR* 3.7 37.0 - - - +
68A PRO* 4.1 8.7 - - + -
210A PRO* 4.0 27.4 - - + -
211A ILE 5.0 0.9 - - - +
278A LEU* 4.7 3.1 - - + -
282A VAL* 4.0 26.9 - - + -
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Residues in contact with ARG 56 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49A ASN 5.0 0.6 + - - -
52A MET* 3.0 38.4 + - - +
53A GLU* 3.1 58.3 + - - +
54A MET 3.2 0.2 - - - -
55A LEU* 1.3 77.4 - - - +
57A GLU* 1.3 60.7 + - + +
59A PHE 3.5 0.3 + - - -
60A GLN 3.1 3.3 + - - -
61A THR* 2.9 50.3 + - + +
62A LYS* 4.6 6.9 + - - +
63A ASN 2.9 27.1 + - - +
64A ARG* 2.8 31.2 + - - +
66A ALA* 4.1 7.6 - - + +
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Residues in contact with GLU 57 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53A GLU* 3.4 12.7 + - - +
54A MET* 3.2 11.8 + - - +
56A ARG* 1.3 74.7 - - + +
58A LEU* 1.3 67.0 + - - +
60A GLN* 3.1 14.7 + - - +
286A LEU* 3.8 31.3 - - + +
290A LEU* 3.4 15.0 - - + +
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Residues in contact with LEU 58 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54A MET 2.9 15.5 + - - +
55A LEU* 3.6 24.5 - - + +
57A GLU* 1.3 77.3 - - - +
59A PHE* 1.3 67.1 + - + +
60A GLN* 3.5 2.4 + - - +
179A ILE* 3.5 40.0 - - + +
180A GLY* 4.0 20.0 - - - +
184A VAL 4.6 1.6 - - - +
202A LEU* 4.1 23.8 - - + -
210A PRO* 5.4 1.8 - - + -
282A VAL* 4.3 15.7 - - + -
285A VAL* 4.1 16.6 - - + -
286A LEU* 4.3 5.1 - - + +
290A LEU* 3.9 17.4 - - + +
294A PHE* 5.9 0.9 - - - -
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Residues in contact with PHE 59 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55A LEU* 3.0 33.3 + - + +
58A LEU* 1.3 83.5 - - + +
60A GLN* 1.3 64.9 + - - +
61A THR* 3.9 8.3 - - + -
175A ALA* 5.0 3.4 - - + -
179A ILE* 3.7 28.3 - - + -
184A VAL* 3.6 6.3 - - + +
186A VAL* 3.1 37.4 + - + +
194A ALA* 3.9 21.1 - - + -
195A ILE 4.5 1.3 - - - -
196A GLY* 3.8 13.2 - - - -
210A PRO* 3.6 41.1 - - + -
211A ILE 4.1 11.7 - - - -
212A THR* 3.6 28.5 - - + -
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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