Contacts of the helix formed by residues 42 - 63 (chain A) in PDB entry 2ILU
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 GLN 42 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18A TRP* 4.6 8.3 - - + -
40A ASP* 2.8 37.7 + - - +
41A GLY* 1.3 80.3 + - - -
43A ALA* 1.3 69.7 + - - +
44A GLU* 3.2 20.6 - - - +
45A ASP* 2.6 33.6 + - - +
46A ALA 3.4 2.6 + - - -
208A ARG* 4.4 1.6 - - - +
211A THR* 3.8 24.7 - - - +
212A VAL* 4.3 7.5 - - - +
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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
----------------------------------------------------------
42A GLN* 1.3 73.1 + - - +
44A GLU* 1.3 65.6 + - - +
46A ALA* 2.8 17.5 + - - +
47A ARG* 3.0 25.9 + - - +
211A THR* 4.3 9.8 + - - +
215A GLU* 3.4 40.5 - - + +
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Residues in contact with GLU 44 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A TRP* 5.6 4.2 - - + -
42A GLN* 3.0 18.9 + - + +
43A ALA* 1.3 76.0 - - - +
45A ASP* 1.3 75.3 + - - +
47A ARG* 3.4 24.3 + - - +
48A LYS* 3.1 32.6 + - - +
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Residues in contact with ASP 45 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A MET* 4.0 24.4 - - + +
11A ILE* 3.7 9.1 - - + +
18A TRP* 3.0 35.2 - - - -
41A GLY* 3.3 1.5 - - - -
42A GLN* 2.6 41.8 + - - +
44A GLU* 1.3 73.4 - - - +
46A ALA* 1.3 64.6 + - - +
48A LYS* 3.2 38.6 + - - +
49A ALA* 3.3 8.7 + - - +
205A VAL* 4.5 4.0 - - + -
212A VAL* 5.4 1.8 - - + -
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Residues in contact with ALA 46 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A GLN 3.4 2.3 + - - +
43A ALA* 2.8 15.3 + - - +
45A ASP* 1.3 74.4 - - - +
47A ARG* 1.3 55.2 + - - +
49A ALA* 3.2 5.7 + - - +
50A ILE* 2.8 33.4 + - + +
174A VAL* 4.7 0.3 - - - +
205A VAL* 4.4 12.7 - - - +
212A VAL* 4.2 14.5 - - + +
215A GLU* 3.4 26.0 - - + -
216A LEU* 4.2 18.4 - - + -
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Residues in contact with ARG 47 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A ALA* 3.0 32.5 + - - +
44A GLU* 3.6 23.8 - - - +
46A ALA* 1.3 73.4 - - - +
48A LYS* 1.3 60.7 + - - +
50A ILE* 4.2 7.4 - - - -
51A ASP* 2.7 43.8 + - - +
215A GLU* 3.2 30.8 + - - +
219A ASN* 3.5 11.6 - - - +
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Residues in contact with LYS 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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11A ILE* 3.9 22.8 - - + +
16A VAL* 6.0 4.4 - - - +
44A GLU* 3.1 28.4 + - - +
45A ASP* 3.2 31.3 + - - +
47A ARG* 1.3 75.8 - - - +
49A ALA* 1.3 62.1 + - - +
51A ASP* 3.5 6.3 + - - +
52A ALA* 3.1 23.2 + - - +
55A ARG* 5.2 0.7 + - - -
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Residues in contact with ALA 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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11A ILE* 3.7 15.8 - - + +
45A ASP 3.3 1.4 + - - -
46A ALA 3.2 8.9 + - - +
47A ARG 3.1 0.6 - - - -
48A LYS* 1.3 76.9 - - - +
50A ILE* 1.3 59.3 - - - +
52A ALA* 3.2 3.6 + - - +
53A ALA* 2.8 28.8 + - - +
174A VAL* 3.6 16.8 - - + -
203A ASN* 3.6 15.6 + - + -
205A VAL* 3.5 29.6 - - + -
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Residues in contact with ILE 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 ALA 2.8 28.2 + - - +
47A ARG* 3.1 5.4 + - - +
49A ALA* 1.3 71.1 - - - +
51A ASP* 1.3 59.3 + - - +
53A ALA* 3.2 3.1 + - - +
54A GLU* 2.8 27.9 + - - +
145A VAL* 4.3 12.5 - - + +
147A THR* 4.9 0.2 - - + -
174A VAL* 4.1 17.9 - - + -
215A GLU* 4.2 8.5 - - + +
216A LEU* 4.6 11.9 - - + -
219A ASN* 3.4 38.6 - - + +
221A LYS* 3.7 32.8 - - + -
222A VAL* 3.8 14.8 - - + -
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Residues in contact with ASP 51 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A ARG* 2.7 30.8 + - - +
48A LYS* 3.8 6.4 - - - +
50A ILE* 1.3 73.6 - - - +
52A ALA* 1.3 57.6 + - - +
54A GLU* 3.5 7.1 - - - +
55A ARG* 2.9 45.8 + - - +
219A ASN* 5.6 1.0 + - - -
221A LYS* 2.7 38.1 + - - +
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Residues in contact with ALA 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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11A ILE* 4.4 0.2 - - + -
12A ASP* 3.6 45.2 - - + +
48A LYS 3.1 14.1 + - - +
49A ALA* 3.5 8.1 - - - +
51A ASP* 1.3 72.5 - - - +
53A ALA* 1.3 68.8 + - - +
55A ARG* 3.2 17.6 + - - +
56A ALA* 3.0 25.8 + - - +
200A GLY* 3.9 4.2 - - - -
203A ASN* 4.2 3.8 - - - +
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Residues in contact with ALA 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 ALA 2.8 14.1 + - - +
50A ILE 3.4 8.5 - - - +
52A ALA* 1.3 77.8 - - - +
54A GLU* 1.3 55.4 + - - +
56A ALA 3.5 0.2 + - - -
57A GLN* 3.0 21.5 + - - +
145A VAL* 3.8 15.3 - - + -
172A THR* 3.0 32.8 + - - +
174A VAL* 3.9 7.9 - - + -
200A GLY 3.3 15.2 + - - +
203A ASN* 3.7 11.4 - - - +
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Residues in contact with GLU 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 ILE 2.8 19.2 + - - +
51A ASP* 3.5 7.7 - - - +
53A ALA* 1.3 71.1 - - - +
55A ARG* 1.3 68.4 + - - +
56A ALA 3.3 0.3 + - - -
57A GLN* 3.4 3.4 + - - +
58A PRO* 3.3 18.9 - - - +
145A VAL* 3.6 17.0 - - + +
221A LYS* 2.7 54.7 + - + +
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Residues in contact with ARG 55 (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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12A ASP* 2.9 35.9 + - - +
48A LYS 5.2 0.8 + - - -
51A ASP* 2.9 41.0 + - + +
52A ALA* 3.2 12.8 + - - +
54A GLU* 1.3 78.2 - - - +
56A ALA* 1.3 60.2 + - - +
58A PRO* 3.6 9.9 - - - +
59A GLU* 5.0 6.6 + - - +
199A ARG* 4.8 2.2 - - - +
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Residues in contact with ALA 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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12A ASP* 5.6 0.2 - - - +
52A ALA 3.0 15.5 + - - +
53A ALA 4.1 1.3 - - - +
55A ARG* 1.3 77.7 - - - +
57A GLN* 1.3 62.7 + - - +
58A PRO* 3.5 0.8 - - - -
59A GLU* 3.7 11.3 + - - +
60A TRP* 3.2 21.8 + - - +
172A THR* 4.1 2.0 - - + -
198A PRO* 6.1 0.4 - - + -
199A ARG* 3.0 29.6 - - + +
200A GLY* 3.9 11.7 - - - -
201A VAL* 4.0 7.1 - - + +
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Residues in contact with GLN 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 ALA 3.0 17.7 + - - +
54A GLU* 3.7 7.4 - - - +
56A ALA* 1.3 73.7 - - - +
58A PRO* 1.3 82.7 - - + +
60A TRP* 3.3 0.7 + - - +
61A GLU* 2.7 50.0 + - - +
142A ALA* 4.2 1.2 - - - +
144A GLY* 3.5 43.8 - - - +
145A VAL* 4.8 0.9 - - + -
170A GLY 3.0 21.4 + - - +
172A THR* 3.4 16.2 - - + +
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Residues in contact with PRO 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 GLU 3.3 15.5 - - - +
55A ARG 3.6 10.8 - - - +
56A ALA 3.7 0.2 - - - -
57A GLN* 1.3 101.6 - - + +
59A GLU* 1.3 60.1 - - + +
61A GLU* 3.4 3.6 + - + +
62A ALA* 2.9 28.9 + - - +
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Residues in contact with GLU 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 ARG 5.0 7.6 - - - +
56A ALA* 3.7 9.1 + - - +
57A GLN 3.4 0.4 - - - -
58A PRO* 1.3 79.9 - - + +
60A TRP* 1.3 63.3 + - - +
62A ALA* 3.1 17.3 + - - +
63A LEU* 3.2 18.2 + - - +
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Residues in contact with TRP 60 (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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56A ALA 3.2 19.2 + - - +
57A GLN* 3.7 5.8 - - - +
58A PRO 3.3 0.2 - - - -
59A GLU* 1.3 74.9 - - - +
61A GLU* 1.3 62.0 + - - +
63A LEU* 3.2 36.1 + - + +
68A ARG* 3.4 31.2 - - + +
71A TRP* 3.5 38.4 - + + -
72A LEU* 5.8 0.9 - - + -
167A LEU* 3.1 33.9 + - + +
170A GLY 3.6 14.8 - - - -
171A ASN 3.2 25.4 + - - -
172A THR* 4.4 1.1 - - + -
197A LEU* 3.8 14.6 - - + -
198A PRO* 3.8 21.3 - - + -
201A VAL* 3.5 36.9 - - + +
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Residues in contact with GLU 61 (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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57A GLN* 2.7 47.5 + - - +
58A PRO* 3.8 3.8 - - + +
60A TRP* 1.3 72.4 - - - +
62A ALA* 1.3 61.4 + - - +
63A LEU 3.0 6.7 - - - +
68A ARG* 3.0 24.5 + - - +
141A ARG* 4.0 11.0 - - - +
142A ALA* 2.9 38.5 + - + +
169A THR 4.5 1.6 - - - +
170A GLY* 3.6 7.9 - - - +
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Residues in contact with ALA 62 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A PRO 2.9 17.7 + - - +
59A GLU* 3.1 11.8 + - - +
61A GLU* 1.3 75.7 - - - +
63A LEU* 1.3 62.6 + - + +
64A PRO* 3.6 6.4 - - - +
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Residues in contact with LEU 63 (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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59A GLU 3.2 14.3 + - - +
60A TRP* 3.2 41.2 + - + +
61A GLU 3.0 3.8 - - - +
62A ALA* 1.3 78.7 - - - +
64A PRO* 1.3 74.6 - - + +
65A ALA 3.3 0.3 + - - -
67A GLU* 3.8 24.2 - - + +
68A ARG* 2.8 31.7 + - + -
71A TRP* 4.4 14.8 - - + +
198A PRO* 5.1 4.0 - - + -
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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