Contacts of the helix formed by residues 60 - 81 (chain A) in PDB entry 1XIL
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 LEU 60 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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41A THR* 3.9 17.6 - - + +
44A LYS* 3.8 41.3 - - + +
45A YOF 3.6 47.1 - - + +
48A ALA* 4.4 4.0 - - + -
56A ALA* 3.0 25.8 + - + +
57A GLN 3.6 5.4 - - - +
58A ILE 3.1 0.2 - - - -
59A ALA* 1.3 76.0 - - + +
61A GLN* 1.3 64.6 + - - +
62A PRO* 3.4 1.1 - - - -
63A ALA* 3.3 11.0 + - + +
64A LEU* 3.0 22.3 + - - +
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Residues in contact with GLN 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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45A YOF 5.0 12.2 + - + -
57A GLN 3.5 13.8 + - - +
58A ILE* 3.1 34.3 + - - +
60A LEU* 1.3 79.4 - - - +
62A PRO* 1.3 68.2 - - + +
64A LEU* 3.1 5.8 + - - +
65A LYS* 2.9 27.6 + - + +
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Residues in contact with PRO 62 (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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58A ILE 3.7 5.4 - - - +
59A ALA* 3.4 17.3 - - - +
60A LEU 3.6 0.4 - - - -
61A GLN* 1.3 94.8 - - + +
63A ALA* 1.3 55.4 + - - +
65A LYS* 4.0 8.4 - - + +
66A PHE* 3.0 32.2 + - - +
119B GLN* 3.6 21.6 + - - +
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Residues in contact with ALA 63 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A THR* 3.7 21.8 + - + +
59A ALA 5.2 0.6 + - - +
60A LEU* 3.3 12.5 + - + +
61A GLN 3.3 0.4 - - - -
62A PRO* 1.3 76.2 - - - +
64A LEU* 1.3 67.9 + - - +
67A ASN* 2.9 41.9 + - - +
119B GLN* 3.8 11.6 - - - +
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Residues in contact with LEU 64 (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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38A LEU* 3.4 30.7 - - + -
41A THR* 3.8 17.7 - - + +
42A GLU* 4.0 18.4 - - + +
45A YOF 5.5 11.9 - - + -
60A LEU 3.0 17.3 + - - +
61A GLN* 3.9 5.6 - - - +
63A ALA* 1.3 79.5 - - - +
65A LYS* 1.3 60.2 + - - +
67A ASN* 5.2 0.2 - - - -
68A GLY* 2.8 33.0 + - - +
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Residues in contact with LYS 65 (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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61A GLN 2.9 15.5 + - - +
62A PRO* 4.0 7.2 - - - +
64A LEU* 1.3 82.7 - - - +
66A PHE* 1.3 59.2 + - - +
69A GLY* 2.8 28.2 + - - +
143A GLN 4.0 2.6 - - - +
144A ASP* 3.1 44.2 + - + +
145A PRO* 4.4 11.4 - - + +
149A THR* 4.6 11.1 - - + +
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Residues in contact with PHE 66 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A PHE* 3.7 23.5 - + - -
62A PRO 3.0 19.2 + - - +
63A ALA 4.1 0.9 - - - +
65A LYS* 1.3 80.4 - - - +
67A ASN* 1.3 75.6 + - - +
70A GLY* 2.8 23.2 + - - -
142A ASN* 4.8 1.3 - - + -
143A GLN* 3.3 31.3 - - + +
144A ASP* 5.8 0.9 - - - -
161A TRP* 3.6 32.3 - + - -
118B VAL 5.5 0.4 - - - -
119B GLN* 3.7 52.9 - - + +
120B GLY 4.4 0.2 - - - -
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Residues in contact with ASN 67 (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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34A PHE* 3.5 41.6 - - - +
37A ASN* 3.3 36.9 + - - +
38A LEU* 3.8 12.3 - - - +
41A THR* 4.7 0.4 + - - -
63A ALA* 2.9 36.5 + - - +
66A PHE* 1.3 86.1 - - - +
68A GLY* 1.3 66.9 + - - +
70A GLY 3.3 0.3 + - - -
71A HIS* 2.9 24.3 + - - +
119B GLN* 5.0 1.6 - - - +
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Residues in contact with GLY 68 (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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38A LEU* 3.8 27.4 - - - +
64A LEU* 2.8 24.7 + - - -
67A ASN* 1.3 72.2 - - - +
69A GLY* 1.3 61.7 + - - +
71A HIS* 3.2 4.5 + - - +
72A ILE* 2.9 32.7 + - - +
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Residues in contact with GLY 69 (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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64A LEU 3.8 0.2 + - - -
65A LYS* 2.8 26.2 + - - +
68A GLY* 1.3 73.8 - - - +
70A GLY* 1.3 61.2 + - - +
72A ILE* 3.6 0.8 - - - +
73A ASN* 2.8 28.9 + - - +
143A GLN 3.3 17.0 - - - -
145A PRO* 4.0 19.5 - - - +
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Residues in contact with GLY 70 (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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34A PHE* 3.7 20.6 - - - -
66A PHE 2.8 22.4 + - - -
67A ASN 3.3 0.8 + - - -
69A GLY* 1.3 72.5 - - - +
71A HIS* 1.3 60.4 + - - +
74A HIS* 2.7 32.5 + - - +
143A GLN* 3.5 20.3 - - - +
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Residues in contact with HIS 71 (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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2A HIS* 4.1 21.5 + + + +
3A SER 3.3 26.6 + - - -
5A PRO* 4.0 4.5 - - + -
31A HIS* 2.7 33.2 + - + +
34A PHE* 4.0 4.8 - - + +
35A VAL* 3.5 9.8 - - + +
38A LEU* 3.7 25.8 - - + -
67A ASN 2.9 13.4 + - - +
68A GLY 3.4 8.1 - - - +
70A GLY* 1.3 74.2 - - - +
72A ILE* 1.3 67.2 + - + +
75A SER* 2.8 46.4 + - - -
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Residues in contact with ILE 72 (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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68A GLY* 2.9 24.8 + - - +
69A GLY 3.6 3.8 - - - +
71A HIS* 1.3 79.3 - - + +
73A ASN* 1.3 74.6 + - - +
75A SER* 3.7 3.9 - - - -
76A ILE* 3.1 41.0 + - + +
125A TRP* 6.1 0.2 - - + -
145A PRO* 3.9 28.3 - - + -
146A LEU 5.8 0.7 - - - +
147A GLN* 6.3 0.7 - - + +
148A GLY* 6.4 0.4 - - - -
154A PRO* 5.9 0.9 - - + -
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Residues in contact with ASN 73 (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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69A GLY 2.8 15.5 + - - +
70A GLY 4.1 0.2 - - - +
72A ILE* 1.3 81.1 - - - +
74A HIS* 1.3 57.7 + - - +
76A ILE* 3.3 3.3 + - - +
77A PHE* 2.9 27.2 + - - +
123A TRP* 3.5 34.9 - - + +
125A TRP* 3.8 23.2 - - + -
143A GLN* 2.9 46.4 + - - +
144A ASP 4.0 3.2 + - - -
145A PRO* 3.4 22.9 - - - +
146A LEU 4.3 0.3 + - - -
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Residues in contact with HIS 74 (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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26A HIS* 3.1 30.5 + + - -
30A HIS* 5.1 0.2 - - - +
31A HIS* 3.6 24.2 - + + +
34A PHE* 3.3 26.7 - + - -
70A GLY* 2.7 29.9 + - - +
73A ASN* 1.3 71.9 - - - +
75A SER* 1.3 65.2 - - - +
77A PHE* 3.1 6.7 + + - +
78A TRP* 3.0 43.0 + + + -
123A TRP* 3.7 8.7 - + - -
143A GLN* 3.5 20.0 - - - -
159A ASP* 3.6 1.5 + - - -
163A HIS* 3.9 0.4 + - - -
500A MN 2.2 29.4 + - - -
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Residues in contact with SER 75 (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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5A PRO* 3.8 11.6 - - - +
31A HIS* 3.3 17.4 - - - -
71A HIS* 2.8 37.8 + - - -
72A ILE* 3.7 4.9 - - - -
74A HIS* 1.3 77.4 - - - +
76A ILE* 1.3 62.9 + - - +
78A TRP* 3.8 8.2 + - - +
79A THR* 3.4 22.0 + - - +
192A ARG* 5.2 0.2 - - - -
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Residues in contact with ILE 76 (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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72A ILE* 3.1 32.1 + - + +
73A ASN 3.6 6.5 - - - +
75A SER* 1.3 78.6 - - - +
77A PHE* 1.3 62.3 + - - +
79A THR* 2.6 22.3 + - - -
80A ASN* 3.0 23.2 + - - +
125A TRP* 3.8 20.6 - - + -
154A PRO* 3.5 33.4 - - + -
155A LEU 5.2 0.7 - - - +
192A ARG* 3.8 35.4 - - - +
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Residues in contact with PHE 77 (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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18A ILE* 5.1 2.0 - - + -
23A MET* 5.9 0.7 - - + -
26A HIS* 4.0 22.4 - + - -
73A ASN 2.9 17.7 + - - +
74A HIS* 3.4 6.5 - + - +
76A ILE* 1.3 75.4 - - - +
78A TRP* 1.3 84.7 + + - +
80A ASN* 3.0 16.5 + - + +
81A LEU* 3.3 43.3 - - + +
123A TRP* 3.7 22.0 - + + -
125A TRP* 6.0 0.2 - - - -
157A GLY* 3.2 27.8 - - - -
159A ASP* 3.8 13.2 - - + -
164A ALA* 5.5 0.4 - - + -
176A YOF 3.7 23.6 - - - -
180A ILE* 3.9 16.2 - - + -
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Residues in contact with TRP 78 (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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5A PRO* 4.5 11.4 - - + -
6A ASP 5.5 0.7 - - - +
7A LEU* 3.3 28.9 - - + -
8A PRO* 4.0 9.1 - - + +
9A YOF 2.8 26.6 + - - +
23A MET* 3.6 31.4 - - + -
26A HIS* 3.5 42.2 - + + -
27A HIS* 3.7 29.4 - + + -
31A HIS* 3.6 18.0 + - + -
74A HIS* 3.0 37.2 + + + -
75A SER* 4.2 9.4 - - - +
76A ILE 3.4 0.2 - - - -
77A PHE* 1.3 96.5 - + - +
79A THR* 1.3 59.7 + - + +
81A LEU* 3.0 15.3 + - + +
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Residues in contact with THR 79 (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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8A PRO* 4.7 12.1 - - + -
75A SER 3.4 14.6 - - - +
76A ILE 2.6 18.6 + - - -
78A TRP* 1.3 76.6 - - + +
80A ASN* 1.3 56.5 + - - +
81A LEU 3.3 2.2 - - - -
185A ASN* 3.2 14.1 + - - +
188A ASN* 3.1 38.8 + - - +
192A ARG* 2.6 25.0 + - - +
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Residues in contact with ASN 80 (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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76A ILE* 3.0 22.7 + - - +
77A PHE* 3.0 12.7 + - - +
79A THR* 1.3 77.5 - - - +
81A LEU* 1.3 57.7 + - + +
155A LEU 3.1 19.2 + - - -
156A LEU* 3.3 18.0 - - + +
157A GLY* 2.9 30.6 + - - +
184A ILE* 3.4 11.6 - - - +
185A ASN* 2.7 29.9 + - - -
188A ASN* 3.0 20.9 + - - -
189A VAL* 4.2 3.4 - - - +
192A ARG* 3.6 8.1 - - - +
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Residues in contact with LEU 81 (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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8A PRO* 4.9 1.0 - - - +
9A YOF 3.2 24.3 - - - +
14A LEU* 3.8 24.2 - - + -
18A ILE* 4.1 9.6 - - + -
23A MET* 4.6 7.2 - - + -
77A PHE* 3.3 47.5 + - + +
78A TRP* 3.0 14.7 + - + +
79A THR* 4.0 4.7 - - - +
80A ASN* 1.3 87.4 - - + +
82A SER* 1.3 66.7 + - - +
157A GLY 5.6 0.7 - - - +
180A ILE* 4.1 26.5 - - + -
183A VAL* 3.2 12.3 - - + +
184A ILE* 4.3 6.7 - - + -
185A ASN* 4.0 1.5 + - - -
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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