Contacts of the helix formed by residues 66 - 85 (chain A) in PDB entry 2X1L
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 PRO 66 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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60A ALA* 4.1 0.2 - - - -
64A GLY 4.8 0.4 - - - +
65A ILE* 1.4 92.6 - - + +
67A ALA* 1.3 65.4 + - - +
68A ALA* 3.3 7.0 - - + +
69A GLU* 3.1 27.0 + - + +
70A LEU* 3.1 12.1 + - - +
513C GLN* 4.8 21.5 - - + +
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Residues in contact with ALA 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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56A MET* 5.0 2.2 - - - +
57A ALA* 4.5 8.5 - - + +
60A ALA* 3.7 19.1 - - + +
65A ILE 3.7 1.0 + - - -
66A PRO* 1.3 72.4 - - - +
68A ALA* 1.3 57.4 + - - +
70A LEU* 3.4 2.6 + - - +
71A ALA* 2.9 30.1 + - - +
215A TRP* 3.6 43.9 + - + +
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Residues in contact with ALA 68 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A PRO* 3.3 5.3 - - + +
67A ALA* 1.3 78.2 - - - +
69A GLU* 1.3 62.1 + - - +
71A ALA* 3.6 2.3 + - - +
72A ARG* 3.1 25.6 + - - +
215A TRP* 3.7 24.7 - - + -
66B PRO* 5.6 10.1 - - + -
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Residues in contact with GLU 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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65A ILE* 3.8 27.8 - - + +
66A PRO* 3.1 25.7 + - + +
68A ALA* 1.3 76.9 - - - +
70A LEU* 1.3 64.8 + - - +
72A ARG* 3.3 32.2 + - - +
73A ARG* 3.0 29.9 + - + +
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Residues in contact with LEU 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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14A PRO 4.5 0.4 - - - +
56A MET* 3.6 42.0 - - + +
59A THR* 3.9 13.7 - - + -
60A ALA* 3.6 17.9 - - + +
63A GLU* 3.5 33.4 - - - +
65A ILE* 3.8 15.0 - - + -
66A PRO 3.1 10.4 + - - +
67A ALA 3.8 6.1 - - - +
69A GLU* 1.3 75.9 - - - +
71A ALA* 1.3 62.4 + - - +
73A ARG* 3.5 9.4 - - - +
74A ASN* 3.0 53.7 + - - +
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Residues in contact with ALA 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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14A PRO* 4.3 1.2 - - - +
51A VAL* 3.6 31.2 - - + -
56A MET* 3.9 15.2 - - + +
67A ALA 2.9 18.4 + - - +
68A ALA* 3.7 4.9 - - - +
70A LEU* 1.3 75.9 - - - +
72A ARG* 1.3 59.6 + - - +
75A SER* 2.7 34.4 + - - -
96A SER* 5.7 2.7 - - - +
215A TRP* 3.9 11.9 - - + -
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Residues in contact with ARG 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 ALA 3.1 15.5 + - - +
69A GLU* 3.3 27.1 + - - +
71A ALA* 1.3 76.3 - - - +
73A ARG* 1.3 80.9 + - - +
76A ASP* 3.1 54.6 + - - +
94A ARG* 3.2 8.3 + - - +
66B PRO* 5.7 4.0 - - - +
68B ALA* 3.6 37.8 + - - +
69B GLU* 3.6 31.0 - - - +
72B ARG* 3.8 13.4 - - - +
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Residues in contact with ARG 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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63A GLU* 2.9 33.1 + - - -
65A ILE* 3.8 18.0 - - - +
69A GLU* 3.0 24.5 + - - +
70A LEU* 3.5 10.3 - - - +
72A ARG* 1.3 96.8 - - - +
74A ASN* 1.3 84.6 + - - +
76A ASP* 3.4 19.8 + - - +
77A VAL* 3.5 13.4 - - + +
80A ARG* 4.8 0.9 + - - +
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Residues in contact with ASN 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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14A PRO* 2.9 36.8 + - + +
15A ASN 3.9 13.1 + - - -
16A GLY* 4.1 12.2 + - - +
63A GLU* 5.2 0.8 + - - -
70A LEU* 3.0 36.2 + - - +
73A ARG* 1.3 101.0 + - - +
75A SER* 1.3 63.7 + - - +
77A VAL* 3.3 13.5 + - + +
78A PHE* 3.2 27.0 + - - -
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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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14A PRO* 3.6 6.6 - - - +
49A THR* 2.8 40.0 + - - -
51A VAL* 3.6 5.5 - - - +
71A ALA 2.7 23.7 + - - -
74A ASN* 1.3 74.4 - - - +
76A ASP* 1.3 60.3 + - - +
78A PHE* 3.2 3.3 + - - +
79A GLN* 2.9 29.5 + - - +
92A PHE* 3.9 3.1 - - - -
94A ARG* 3.6 25.4 - - - -
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Residues in contact with ASP 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 ARG* 3.1 35.8 + - - +
73A ARG* 3.4 10.5 - - - +
75A SER* 1.3 76.3 - - - +
77A VAL* 1.3 56.2 + - - +
79A GLN* 3.5 7.2 + - - +
80A ARG* 3.0 57.0 + - - +
94A ARG* 2.7 31.9 + - - +
72B ARG* 3.8 13.7 + - - -
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Residues in contact with VAL 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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17A VAL* 5.4 6.5 - - + -
18A PRO* 3.8 24.2 - - + -
73A ARG* 3.5 18.8 - - + +
74A ASN* 3.5 15.3 - - - +
75A SER 3.2 0.6 - - - -
76A ASP* 1.3 76.1 - - - +
78A PHE* 1.3 57.9 + - - +
80A ARG* 3.5 23.2 + - + +
81A LEU* 3.1 27.8 + - + +
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Residues in contact with PHE 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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12A ALA* 3.9 7.6 - - + -
13A TYR 4.2 10.1 - - - -
14A PRO* 3.7 20.9 - - + -
16A GLY 3.6 22.2 - - - -
17A VAL 4.5 0.9 - - - -
18A PRO* 3.7 39.3 - - + -
22A HIS* 3.8 26.5 - + - -
26A TYR* 3.5 29.8 - + - -
49A THR* 3.9 16.4 - - + -
74A ASN 3.2 20.8 + - - -
75A SER 3.2 8.6 + - - +
77A VAL* 1.3 76.7 - - - +
79A GLN* 1.3 63.9 + - - +
81A LEU* 3.5 4.0 + - - +
82A GLN* 3.3 27.3 + - - +
92A PHE* 4.0 5.6 - - + -
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Residues in contact with GLN 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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75A SER 2.9 16.0 + - - +
76A ASP* 3.8 5.7 - - - +
78A PHE* 1.3 76.1 - - - +
80A ARG* 1.3 59.5 + - + +
82A GLN* 3.2 4.7 + - - +
83A GLU* 3.0 51.5 + - - +
89A PHE* 4.4 10.1 - - + -
92A PHE* 3.6 43.5 - - + +
94A ARG* 3.0 23.9 + - - -
72B ARG* 4.7 8.1 - - - +
76B ASP* 5.6 6.3 + - - -
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Residues in contact with ARG 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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73A ARG* 4.8 0.8 + - - +
76A ASP* 3.0 39.9 + - - +
77A VAL* 3.8 31.8 - - - +
79A GLN* 1.3 73.8 - - + +
81A LEU* 1.3 60.2 + - - +
83A GLU* 3.4 19.8 + - - +
84A LYS* 2.9 28.4 + - - +
96B SER 5.9 0.8 + - - -
97B ASP* 6.1 1.8 - - - +
98B ALA* 5.9 8.8 - - - +
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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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18A PRO* 3.5 31.2 - - + -
23A ALA* 4.8 4.9 - - + +
26A TYR* 4.3 19.5 - - + -
77A VAL 3.1 17.6 + - - +
78A PHE* 3.6 5.6 - - + +
79A GLN 3.2 0.4 - - - -
80A ARG* 1.3 76.9 - - - +
82A GLN* 1.3 51.3 + - - +
84A LYS* 3.0 10.1 + - + +
85A LEU* 2.7 60.1 + - + +
312A PRO* 3.7 33.9 - - + -
313A VAL* 3.9 22.9 - - + +
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Residues in contact with GLN 82 (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 TYR* 3.5 44.1 + - + +
45A TYR* 4.7 0.2 + - - -
47A THR* 3.0 39.7 + - - +
48A GLY 4.6 1.4 + - - +
78A PHE* 3.3 12.6 + - - +
79A GLN* 3.2 7.9 + - - +
81A LEU* 1.3 76.7 - - + +
83A GLU* 1.3 59.6 + - - +
85A LEU* 4.3 1.8 - - - -
86A ASN 3.2 4.0 + - - -
87A ILE* 2.9 62.8 + - + +
89A PHE* 3.8 13.0 - - + -
92A PHE* 3.6 14.7 - - + -
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Residues in contact with GLU 83 (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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79A GLN* 3.0 38.4 + - - +
80A ARG* 3.5 26.7 - - - +
81A LEU 3.2 0.2 - - - -
82A GLN* 1.3 78.1 - - - +
84A LYS* 1.3 59.4 + - - +
86A ASN* 3.3 12.1 + - - -
87A ILE 5.0 1.6 - - - +
89A PHE* 4.3 15.1 - - + -
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Residues in contact with LYS 84 (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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80A ARG 2.9 14.5 + - - +
81A LEU* 3.0 12.3 + - + +
83A GLU* 1.3 73.5 - - - +
85A LEU* 1.3 61.3 + - + +
86A ASN 3.2 3.6 + - - -
313A VAL* 3.5 31.7 - - + +
316A VAL* 4.0 23.5 - - + +
317A ASP* 2.8 39.7 + - - -
321A LEU* 3.4 18.6 - - - +
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Residues in contact with LEU 85 (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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23A ALA* 3.8 33.9 - - + +
26A TYR* 4.5 10.8 - - + -
27A ILE* 4.0 21.5 - - + -
81A LEU* 2.7 45.4 + - + +
82A GLN* 4.6 1.3 - - - -
83A GLU 3.3 0.4 - - - -
84A LYS* 1.3 72.1 - - + +
86A ASN* 1.3 64.4 + - - +
87A ILE* 3.3 14.5 - - + +
312A PRO* 4.9 2.9 - - + -
316A VAL* 3.9 27.4 - - + -
321A LEU* 3.6 15.0 - - + +
324A VAL* 5.6 1.8 - - + -
325A ARG* 2.9 25.6 + - - -
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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