Contacts of the strand formed by residues 68 - 87 (chain B) in PDB entry 2I5T
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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53B PHE* 3.3 3.6 - - - -
54B GLY 2.9 38.9 + - - +
56B SER* 5.7 2.0 - - - +
61B SER* 3.9 24.9 - - - +
64B TRP* 3.7 34.1 - - + -
66B GLY 3.9 1.8 - - - +
67B GLY* 1.3 78.4 - - - +
69B ALA* 1.3 66.4 + - - +
70B THR 3.6 0.3 + - - -
104B MSE 4.1 18.2 - - + -
105B TYR* 3.3 30.3 - - + +
127B MSE 4.2 9.6 - - - +
139B TYR* 3.5 13.0 - - + +
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Residues in contact with ALA 69 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B TYR* 3.8 19.8 - - + -
23B GLY* 4.1 16.6 - - - -
51B LEU* 4.2 5.8 - - + -
52B ASP 3.4 6.7 - - - -
53B PHE* 3.7 17.3 - - + -
68B ILE* 1.3 73.9 - - - +
70B THR* 1.3 60.1 + - - +
105B TYR* 2.7 30.2 + - - +
127B MSE 4.8 0.2 - - - +
139B TYR* 3.0 21.7 + - + +
143B ILE* 4.7 0.2 - - + -
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Residues in contact with THR 70 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22B TYR* 3.4 9.4 - - - -
51B LEU* 3.5 2.8 - - - +
52B ASP* 2.7 43.3 + - + +
54B GLY 4.8 0.2 - - - +
68B ILE 4.4 1.1 - - - +
69B ALA* 1.3 76.4 - - - +
71B ILE* 1.3 75.9 + - - +
126B LEU 3.8 0.2 - - - -
127B MSE 2.8 53.3 + - + +
130B TYR* 3.6 35.4 - - + +
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Residues in contact with ILE 71 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128A THR* 5.0 0.3 - - - -
20B PHE* 5.3 0.7 - - + -
22B TYR* 3.7 45.1 + - + +
46B LEU* 3.5 29.2 - - + -
49B PHE* 3.7 15.0 - - + -
50B LYS 3.2 9.2 - - - +
51B LEU* 4.2 2.2 - - - -
52B ASP 4.6 0.2 - - - +
70B THR* 1.3 86.1 + - - +
72B PHE* 1.3 64.2 + - - +
79B VAL* 3.8 25.1 - - + -
108B ILE* 4.1 17.5 - - + -
110B VAL* 5.2 0.2 - - + -
124B SER* 5.0 1.3 - - - +
126B LEU* 3.5 27.3 - - + +
127B MSE 4.8 1.7 - - - +
130B TYR* 5.9 0.6 - - - -
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Residues in contact with PHE 72 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128A THR* 3.6 26.2 - - - +
129A ASN* 4.0 20.6 - - - -
49B PHE* 3.2 9.3 - - - -
50B LYS* 2.8 58.6 + - + -
52B ASP* 3.8 26.5 - - + -
71B ILE* 1.3 78.4 - - - +
73B GLN* 1.3 74.0 + - - +
74B SER* 4.1 14.6 - - - -
130B TYR* 3.6 23.1 - + + +
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Residues in contact with GLN 73 (chain B).
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* 3.5 7.0 + - - +
100A VAL* 4.1 6.1 + - - +
103A GLY* 3.3 38.7 - - - +
104A MSE 4.3 0.3 - - - -
105A TYR* 2.9 36.6 + - - -
106A VAL* 3.6 12.2 - - - +
128A THR* 2.7 35.9 + - - +
129A ASN* 2.8 35.3 + - + +
48B ASP 3.4 8.3 - - - +
49B PHE* 3.4 29.2 - - + -
72B PHE* 1.3 71.6 - - - +
74B SER* 1.3 53.3 - - - +
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Residues in contact with SER 74 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129A ASN* 4.4 3.6 - - - +
48B ASP* 2.9 19.9 + - - -
50B LYS* 3.8 23.7 + - - +
72B PHE* 3.6 9.1 + - - -
73B GLN* 1.3 75.0 - - - +
75B PRO* 1.3 77.5 + - - +
76B GLY 3.2 0.2 + - - -
77B ASP* 2.4 41.5 + - - +
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Residues in contact with PRO 75 (chain B).
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* 3.6 32.1 - - + +
59A LYS* 6.1 3.1 - - - +
102A SER 4.8 10.5 - - - +
103A GLY* 6.0 0.7 - - - -
48B ASP* 3.7 17.0 - - + +
74B SER* 1.3 88.3 + - - +
76B GLY* 1.3 59.0 + - - +
77B ASP* 3.4 2.9 + - - +
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Residues in contact with GLY 76 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47B GLN* 4.2 6.2 + - - -
48B ASP* 2.9 14.8 + - - -
75B PRO* 1.3 72.4 - - - +
77B ASP* 1.3 64.4 + - - +
78B GLU* 5.8 0.3 - - - +
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Residues in contact with ASP 77 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47B GLN* 3.0 7.7 + - - -
48B ASP 2.7 30.7 + - - -
49B PHE 3.2 18.6 - - - +
50B LYS* 3.6 27.2 + - + +
74B SER* 2.4 34.6 + - - +
75B PRO 3.3 2.1 - - - +
76B GLY* 1.3 80.1 - - - +
78B GLU* 1.3 58.4 + - - +
159B LYS* 5.6 4.3 + - - -
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Residues in contact with GLU 78 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45B ARG* 3.4 23.8 - - + -
46B LEU 3.4 9.6 - - - +
47B GLN* 3.7 12.5 + - - +
49B PHE 3.3 9.9 - - - +
50B LYS* 4.9 1.4 - - - -
51B LEU* 5.0 1.0 + - - +
77B ASP* 1.3 79.8 + - - +
79B VAL* 1.3 64.5 + - - +
80B TRP* 3.0 30.9 + - + +
156B TYR* 4.0 13.4 - - + -
159B LYS* 5.5 11.1 + - - +
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Residues in contact with VAL 79 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B PHE* 3.9 8.3 - - + -
22B TYR* 3.7 31.2 - - + -
45B ARG* 3.4 1.0 - - - -
46B LEU* 2.6 47.8 + - + +
49B PHE* 3.5 17.3 - - + +
50B LYS 3.7 3.1 - - - -
51B LEU* 3.5 28.3 - - + +
71B ILE* 3.8 18.2 - - + -
78B GLU* 1.3 80.2 - - - +
80B TRP* 1.3 66.0 + - - +
156B TYR* 3.8 12.6 - - - +
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Residues in contact with TRP 80 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B PHE* 4.0 3.1 - - - -
22B TYR* 4.3 6.9 - - - +
26B LEU* 4.5 0.5 - - - +
43B VAL* 3.8 14.8 - - + -
44B ALA* 3.4 27.4 - - - -
45B ARG* 3.7 34.3 - - + -
78B GLU* 3.0 28.7 + - + -
79B VAL* 1.3 83.1 - - - +
81B GLY* 1.3 59.4 + - - +
113B ALA 4.7 2.2 - - - -
114B THR 5.7 0.2 - - - -
115B GLN* 3.5 35.4 - - + -
152B LEU* 3.8 11.8 - - + +
153B PRO* 3.5 34.4 - - + +
156B TYR* 3.5 57.9 + + + +
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Residues in contact with GLY 81 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20B PHE* 3.5 11.6 - - - -
21B ALA 3.2 14.8 - - - -
26B LEU* 3.6 8.7 - - - -
43B VAL* 3.4 8.3 - - - +
44B ALA 2.9 32.0 + - - -
80B TRP* 1.3 76.0 - - - +
82B VAL* 1.3 64.8 + - - -
152B LEU* 4.3 3.8 - - - +
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Residues in contact with VAL 82 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19B TYR 3.4 1.6 - - - +
20B PHE* 3.5 0.8 - - - -
21B ALA* 2.7 37.1 + - - +
26B LEU* 3.6 22.0 - - + +
40B PHE* 3.6 21.5 - - + -
42B CYS 3.6 2.9 - - - -
43B VAL* 4.3 3.4 - - + -
81B GLY* 1.3 76.5 - - - +
83B VAL* 1.3 72.2 - - - +
84B TRP* 3.4 36.2 - - + +
150B ASN* 3.6 31.4 - - + +
152B LEU* 4.1 7.4 - - + -
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Residues in contact with VAL 83 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18B LEU* 3.8 29.2 - - + -
19B TYR 3.2 4.0 - - - +
20B PHE* 3.9 15.0 - - + -
41B PHE* 2.8 47.5 + - + +
42B CYS* 2.8 29.7 + - - +
44B ALA* 4.0 17.9 - - + -
82B VAL* 1.3 79.4 - - - +
84B TRP* 1.3 56.2 + - - +
112B VAL* 4.2 2.0 - - + -
120B ILE* 4.5 2.0 - - + -
122B CYS* 3.8 22.9 - - - -
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Residues in contact with TRP 84 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17B PHE 3.7 0.3 - - - +
18B LEU* 3.4 3.8 - - - -
19B TYR* 2.8 43.7 + + + +
21B ALA* 3.8 10.1 - - + +
25B ASN 2.8 27.3 + - - -
26B LEU 4.1 8.1 - - - -
28B THR* 3.4 42.0 - - + -
31B ILE* 3.5 38.3 - - + +
32B HIS* 4.6 1.1 - - - -
38B ALA* 4.2 15.3 - - + -
39B ALA 3.4 12.1 - - - -
40B PHE* 3.4 41.1 - + + -
41B PHE* 4.3 2.2 - - - -
82B VAL* 3.4 37.0 - - + +
83B VAL* 1.3 72.5 - - - +
85B LYS* 1.3 60.6 + - - +
86B MSE 4.4 2.2 - - + -
150B ASN* 4.1 3.4 - - - -
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Residues in contact with LYS 85 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16B SER* 3.7 30.6 + - - +
17B PHE 3.6 2.9 - - - +
18B LEU* 4.0 18.2 - - + -
37B SER 4.1 2.1 - - - +
38B ALA* 3.5 2.3 - - - -
39B ALA* 2.7 46.7 + - + +
40B PHE 5.5 0.4 - - - +
41B PHE* 4.1 25.9 - - + +
84B TRP* 1.3 71.2 - - - +
86B MSE 1.3 64.7 + - - +
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Residues in contact with MSE 86 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16B SER* 3.2 8.6 - - - -
17B PHE* 2.7 58.4 + - + +
19B TYR* 4.1 24.9 - - + -
31B ILE* 4.5 4.7 - - - -
35B ASN* 3.4 35.9 - - + +
37B SER* 5.3 4.5 - - - +
38B ALA* 4.2 21.1 - - + +
84B TRP 4.3 10.1 - - - +
85B LYS* 1.3 80.3 - - - +
87B ASN* 1.3 59.7 + - - +
90B ASN* 3.9 25.1 - - + +
94B LEU* 4.2 16.6 - - + -
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Residues in contact with ASN 87 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15B GLU* 3.5 22.1 + - - +
16B SER* 4.4 6.6 + - - -
17B PHE* 3.2 12.5 - - - -
37B SER* 3.7 21.9 + - - -
86B MSE 1.3 71.3 - - - +
88B LYS* 1.3 56.1 + - - +
89B SER* 3.3 22.7 + - - +
90B ASN* 2.8 35.1 + - - +
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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