Contacts of the strand formed by residues 68 - 87 (chain A) in PDB entry 2Q53
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 ILE 68 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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53A PHE* 3.3 4.5 - - - -
54A GLY 2.9 36.2 + - - +
55A ASN* 5.7 0.2 - - - -
56A SER* 4.6 10.1 - - - +
61A SER* 3.8 30.1 - - - +
64A TRP* 4.1 19.1 - - + -
66A GLY 3.9 1.8 - - - +
67A GLY* 1.3 77.5 - - - +
69A ALA* 1.3 64.6 + - - +
70A THR 3.6 0.3 + - - -
104A MSE 5.5 5.6 - - + -
105A TYR* 3.5 28.3 - - + +
127A MSE 3.8 24.4 - - - +
139A TYR* 3.8 7.4 - - + +
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Residues in contact with ALA 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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22A TYR* 4.1 18.3 + - + -
23A GLY* 4.4 13.2 - - - -
51A LEU* 4.4 6.3 - - + -
52A ASP 3.5 7.6 - - - +
53A PHE* 3.8 17.5 - - + -
68A ILE* 1.3 72.2 - - - +
70A THR* 1.3 58.8 + - - +
105A TYR* 2.6 31.6 + - - +
139A TYR* 3.0 24.5 + - + +
143A ILE* 4.7 0.4 - - + -
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Residues in contact with THR 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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22A TYR* 3.5 8.1 - - - -
51A LEU* 3.8 1.4 - - - +
52A ASP* 3.0 38.6 + - + +
53A PHE 4.7 0.2 - - - +
68A ILE 4.4 0.9 - - - +
69A ALA* 1.3 76.8 - - - +
71A ILE* 1.3 82.1 + - - +
105A TYR* 4.8 0.2 - - - -
126A LEU* 3.7 1.0 - - - -
127A MSE 3.0 53.1 + - + -
130A TYR* 3.7 35.4 - - + +
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Residues in contact with ILE 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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20A PHE* 5.6 0.2 - - + -
22A TYR* 3.4 47.3 + - + +
46A LEU* 3.6 29.4 - - + -
49A PHE* 3.9 13.5 - - + -
50A LYS 3.3 14.8 - - - +
51A LEU* 4.0 3.1 - - - -
70A THR* 1.3 90.0 + - - +
72A PHE* 1.3 66.7 + - - +
79A VAL* 3.9 17.7 - - + -
108A ILE* 4.4 13.5 - - + -
110A VAL* 5.4 0.4 - - + -
124A SER* 5.1 0.4 - - - +
126A LEU* 3.6 25.5 - - + +
127A MSE 4.9 2.1 - - - +
130A TYR* 5.9 0.7 - - - -
128B THR* 4.8 1.4 - - - -
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Residues in contact with PHE 72 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A PHE* 3.2 9.1 - - - -
50A LYS* 2.8 56.8 + - + -
52A ASP* 4.1 19.7 - - + -
71A ILE* 1.3 78.8 - - - +
73A GLN* 1.3 62.5 + - - +
74A SER* 3.8 17.3 - - - -
130A TYR* 3.7 27.4 - + + -
128B THR* 3.7 27.6 - - - +
129B ASN* 3.5 28.7 - - - -
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Residues in contact with GLN 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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48A ASP* 3.1 10.3 - - + +
49A PHE* 3.4 24.5 - - + -
72A PHE* 1.3 71.1 - - - +
74A SER* 1.3 58.2 + - - +
57B GLN* 2.8 28.6 + - - +
100B VAL* 4.3 4.6 + - - +
103B GLY* 3.1 39.8 + - - +
105B TYR 3.3 20.8 + - - -
106B VAL* 3.8 18.8 + - - +
128B THR* 2.8 41.2 + - - +
129B ASN* 3.0 21.9 + - + +
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Residues in contact with SER 74 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A ASP* 2.6 28.1 + - - -
50A LYS* 3.7 24.8 - - - +
72A PHE* 3.4 12.2 + - - -
73A GLN* 1.3 75.6 - - - +
75A PRO* 1.3 73.5 + - - +
77A ASP* 2.7 31.7 + - - +
57B GLN* 3.8 0.2 - - - +
129B ASN* 4.7 2.8 + - - +
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Residues in contact with PRO 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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48A ASP* 3.8 19.5 - - + +
74A SER* 1.3 85.8 + - - +
76A GLY* 1.3 58.5 + - - +
77A ASP* 3.2 10.6 + - - +
57B GLN* 3.5 26.5 - - + +
59B LYS* 5.0 12.8 - - - +
102B SER 4.9 7.4 - - - +
129B ASN* 5.8 0.2 - - - +
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Residues in contact with GLY 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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47A GLN* 3.3 19.5 + - - +
48A ASP* 4.0 2.8 + - - -
74A SER 3.4 0.6 + - - -
75A PRO* 1.3 71.1 - - - +
77A ASP* 1.3 63.2 + - - +
78A GLU* 4.8 4.0 - - - +
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Residues in contact with ASP 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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47A GLN* 2.9 8.5 + - - -
48A ASP 2.9 22.7 + - - -
49A PHE 3.5 12.8 - - - +
50A LYS* 3.1 42.2 + - + +
74A SER* 2.7 35.2 + - - +
75A PRO 3.4 5.7 - - - +
76A GLY* 1.3 75.8 - - - +
78A GLU* 1.3 60.6 + - - +
159A LYS* 5.2 8.2 + - - +
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Residues in contact with GLU 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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45A ARG* 3.4 31.3 + - + -
46A LEU 3.3 8.7 - - - +
47A GLN* 3.7 11.4 - - - +
49A PHE 3.3 9.3 - - - +
50A LYS* 5.1 1.4 - - - -
51A LEU* 5.1 1.6 + - - +
76A GLY 5.0 3.3 - - - +
77A ASP* 1.3 81.1 - - - +
79A VAL* 1.3 61.9 + - - +
80A TRP* 2.7 33.0 + - + +
155A GLU* 5.5 2.4 - - - +
156A TYR* 3.6 15.6 - - + -
159A LYS* 5.4 10.3 + - + +
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Residues in contact with VAL 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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20A PHE* 4.2 4.9 - - + -
22A TYR* 3.5 39.7 - - + -
44A ALA 4.0 0.3 - - - +
45A ARG* 3.5 0.9 - - - -
46A LEU* 2.6 50.0 + - + +
49A PHE* 3.2 24.7 - - + +
50A LYS 3.8 1.3 - - - -
51A LEU* 3.7 25.1 - - + +
71A ILE* 3.9 12.3 - - + -
78A GLU* 1.3 75.6 - - - +
80A TRP* 1.3 64.9 + - - +
81A GLY 4.2 0.2 + - - -
156A TYR* 3.7 10.8 - - - +
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Residues in contact with TRP 80 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A TYR* 4.1 6.9 - - - +
26A LEU* 4.5 0.9 - - - +
43A VAL* 3.9 8.5 - - + -
44A ALA* 3.2 27.8 - - - -
45A ARG* 3.4 40.4 - - + +
78A GLU* 2.7 27.8 + - - -
79A VAL* 1.3 83.9 - - - +
81A GLY* 1.3 57.9 + - - +
113A ALA 4.6 2.2 - - - -
114A THR 5.4 0.2 - - - -
115A GLN* 3.4 39.3 - - + -
152A LEU* 3.3 20.1 - - + +
153A PRO* 3.5 29.7 - - + +
156A TYR* 3.4 59.3 + + + +
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Residues in contact with GLY 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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20A PHE* 3.6 14.9 - - - -
21A ALA 3.2 15.7 - - - -
22A TYR* 4.4 0.2 - - - -
26A LEU* 3.9 8.7 - - - -
43A VAL* 3.5 9.4 - - - +
44A ALA 3.0 24.7 + - - -
80A TRP* 1.3 75.6 - - - +
82A VAL* 1.3 69.8 + - - +
152A LEU* 3.6 2.4 - - - +
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Residues in contact with VAL 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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19A TYR 3.5 2.1 - - - +
20A PHE* 3.6 3.1 - - - -
21A ALA 3.1 29.3 + - - +
25A ASN 5.3 0.2 - - - +
26A LEU* 4.1 10.5 - - + +
40A PHE* 3.5 28.3 - - + -
42A CYS 3.3 3.1 - - - -
43A VAL* 4.1 6.7 - - + -
44A ALA 4.8 0.2 - - - +
81A GLY* 1.3 80.1 - - - +
83A VAL* 1.3 69.8 + - - +
84A TRP* 3.4 33.0 + - + +
150A ASN* 3.7 24.2 - - + +
152A LEU* 3.7 18.2 - - + -
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Residues in contact with VAL 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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18A LEU* 3.9 17.7 - - + -
19A TYR 3.4 4.7 - - - +
20A PHE* 4.1 11.4 - - + -
41A PHE* 2.7 54.7 + - + +
42A CYS* 2.5 40.2 + - - +
44A ALA* 4.1 11.4 - - + -
82A VAL* 1.3 76.6 - - - +
84A TRP* 1.3 54.3 + - - +
112A VAL* 4.3 2.5 - - + -
120A ILE* 4.6 4.3 - - + -
122A CYS* 3.7 32.8 - - - -
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Residues in contact with TRP 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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18A LEU* 3.6 1.8 - - - -
19A TYR* 2.7 51.6 + + + +
21A ALA* 4.8 1.3 - - + -
25A ASN 3.1 20.3 + - - -
26A LEU 4.8 0.2 + - - -
28A THR* 3.3 42.0 - - + -
31A ILE* 3.7 35.9 - - + -
32A HIS* 4.2 6.7 - + - -
38A ALA* 3.7 23.6 - - + -
39A ALA 3.3 15.3 - - - -
40A PHE* 3.2 41.7 - + + -
41A PHE* 4.3 1.6 - - - -
82A VAL* 3.4 30.3 - - + +
83A VAL* 1.3 72.8 - - - +
85A LYS* 1.3 62.0 + - - +
86A MSE 3.6 3.0 + - + +
150A ASN* 4.1 13.2 - - - -
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Residues in contact with LYS 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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14A GLU 5.7 6.0 - - - +
16A SER* 3.9 29.4 - - - +
17A PHE 3.6 3.8 - - - +
18A LEU* 4.0 18.8 - - + -
37A SER 4.4 1.7 - - - +
38A ALA* 3.8 1.0 - - - -
39A ALA* 2.7 47.2 + - + +
41A PHE* 4.0 31.0 - - + +
84A TRP* 1.3 71.7 - - - +
86A MSE 1.3 60.8 - - - +
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Residues in contact with MSE 86 (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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16A SER* 2.9 8.7 - - - -
17A PHE* 2.6 62.3 + - + +
19A TYR* 3.8 22.0 - - - -
31A ILE* 4.9 5.8 - - - -
35A ASN* 3.5 35.4 - - + +
37A SER* 5.5 2.9 - - - +
38A ALA* 4.1 17.9 - - + +
84A TRP* 4.2 4.7 - - + +
85A LYS* 1.3 79.7 - - - +
87A ASN* 1.3 58.7 + - - +
90A ASN* 3.7 24.0 - - + +
94A LEU* 3.7 28.5 - - + -
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Residues in contact with ASN 87 (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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15A GLU* 4.1 20.9 + - - +
16A SER* 3.8 12.3 + - - +
17A PHE* 3.0 10.4 - - - -
37A SER* 5.3 5.8 + - - +
86A MSE 1.3 73.3 - - - +
88A LYS* 1.3 63.4 + - - +
89A SER* 2.6 40.6 + - - +
90A ASN* 2.5 38.6 + - - +
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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