Contacts of the strand formed by residues 71 - 85 (chain B) in PDB entry 5JTO
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 GLU 71 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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27B ASN* 2.9 25.4 + - - +
30B HIS 3.6 8.7 - - - +
31B VAL* 3.6 4.0 + - - -
33B GLN* 3.1 31.2 + - - -
34B LYS* 2.9 38.6 + - + +
67B SER* 3.3 6.8 - - - -
68B LEU 3.0 37.2 + - - +
70B GLU* 1.4 80.3 - - - +
72B THR* 1.3 61.8 + - - +
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Residues in contact with THR 72 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B PRO* 3.9 19.3 - - + +
27B ASN* 2.8 33.8 + - - +
31B VAL* 3.1 11.7 - - - +
66B ALA 3.5 14.1 - - - +
67B SER* 3.9 4.4 - - - -
68B LEU 4.6 0.7 - - - -
71B GLU* 1.3 77.8 - - - +
73B ALA* 1.3 63.5 + - - +
74B PHE 3.7 8.1 - - - +
75B LEU* 3.6 35.1 - - + +
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Residues in contact with ALA 73 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B ALA* 4.8 5.9 - - - +
27B ASN* 4.7 2.8 - - - +
28B ALA* 5.5 0.7 - - - -
31B VAL* 3.7 13.4 - - + +
38B PRO* 3.8 6.5 - - + -
66B ALA* 2.9 27.3 + - + +
67B SER* 3.5 2.0 - - - +
68B LEU* 3.5 24.7 - - + -
72B THR* 1.3 76.2 - - - +
74B PHE* 1.3 73.5 + - + +
123B PHE* 3.3 22.6 - - + -
297H TYR* 6.6 0.4 - - + -
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Residues in contact with PHE 74 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B PHE* 3.8 34.8 - + + -
24B GLU 3.9 5.8 - - - +
25B ALA* 5.0 2.0 - - + +
38B PRO* 4.6 10.8 - - + -
40B VAL* 5.2 3.1 - - + -
64B VAL* 4.2 10.5 - - + -
65B THR 3.9 0.2 - - - -
66B ALA* 3.0 49.1 + - + +
72B THR* 3.7 2.4 - - - +
73B ALA* 1.3 86.9 - - + +
75B LEU* 1.3 67.2 + - - +
76B CYS* 4.9 2.7 - - + -
118B VAL* 3.7 23.6 - - + -
123B PHE* 3.8 34.5 - + + -
126B LEU* 3.9 22.0 - - + -
296H THR* 5.1 11.0 - - + -
297H TYR* 6.1 2.2 - + - -
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Residues in contact with LEU 75 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B PHE* 3.1 12.4 - - - -
24B GLU* 2.9 69.9 + - + +
26B PRO* 4.3 10.8 - - + -
64B VAL 3.8 2.7 - - - -
65B THR* 3.7 32.3 - - + +
72B THR* 3.6 30.7 - - + +
74B PHE* 1.3 74.1 - - - +
76B CYS* 1.3 61.1 + - - +
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Residues in contact with CYS 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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22B SER 3.3 12.8 - - - -
23B PHE* 3.8 17.9 - - + -
24B GLU* 4.3 2.0 + - - -
63B THR* 3.5 5.2 - - - +
64B VAL* 2.8 44.4 + - + +
74B PHE* 4.9 5.6 - - + -
75B LEU* 1.3 76.1 - - - +
77B GLU* 1.3 75.8 + - - +
78B VAL* 4.5 2.2 - - - -
114B ILE* 3.8 43.1 - - + -
117B MET* 4.2 9.0 - - - -
118B VAL* 5.1 0.2 - - + -
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Residues in contact with GLU 77 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B ASP* 3.9 15.7 - - - +
21B ILE* 3.4 4.3 - - - +
22B SER* 2.9 44.9 + - - +
61B ARG* 2.9 40.7 + - + +
62B VAL 3.6 7.2 - - - +
63B THR* 3.1 33.5 + - + +
76B CYS* 1.3 78.9 - - - +
78B VAL* 1.3 69.6 + - - +
79B GLN* 4.5 1.9 - - - +
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Residues in contact with VAL 78 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18B THR* 4.6 0.2 - - + -
20B ASP 3.5 4.5 - - - -
21B ILE* 3.5 27.8 - - + -
60B LEU 4.0 0.2 - - - +
61B ARG* 3.3 7.3 - - - +
62B VAL 3.0 32.0 + - - +
76B CYS* 4.5 4.0 - - - -
77B GLU* 1.3 76.9 - - - +
79B GLN* 1.3 67.6 + - - +
80B GLN* 3.9 15.9 - - - +
110B ALA* 3.8 32.3 - - + +
113B CYS* 3.8 7.0 - - + -
114B ILE* 3.4 37.7 - - + +
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Residues in contact with GLN 79 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18B THR* 3.9 1.4 - - - -
19B LYS* 3.0 32.1 + - + +
20B ASP* 2.9 44.8 + - + +
47B ALA* 5.5 3.5 - - - +
59B VAL* 3.7 21.7 - - + +
60B LEU 3.8 4.9 - - - -
61B ARG* 3.1 50.5 + - + +
77B GLU* 4.5 1.8 - - - +
78B VAL* 1.3 77.5 - - - +
80B GLN* 1.3 61.0 + - - +
81B GLY 3.4 2.4 + - - -
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Residues in contact with GLN 80 (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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120A ARG 4.6 1.2 - - - +
16B ILE* 3.5 19.4 - - + +
17B TYR* 3.2 22.5 + - - -
18B THR* 3.0 25.0 + - - +
59B VAL* 4.5 0.2 - - - -
60B LEU 3.1 29.9 + - - +
78B VAL* 3.9 7.7 - - - +
79B GLN* 1.3 69.0 - - - +
81B GLY* 1.3 61.1 + - - +
106B LEU* 3.4 45.0 - - + +
109B TYR* 3.5 21.6 + - + +
110B ALA* 3.7 27.3 - - + +
113B CYS* 4.8 0.6 - - - +
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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
----------------------------------------------------------
16B ILE* 3.6 2.8 - - - +
17B TYR* 2.9 40.1 + - - +
19B LYS* 3.7 14.7 - - - +
57B GLU* 3.6 10.5 - - - -
58B VAL 3.5 6.7 - - - -
59B VAL* 3.9 4.0 - - - -
79B GLN 3.4 5.9 + - - -
80B GLN* 1.3 76.0 - - - +
82B GLY* 1.3 59.2 + - - -
106B LEU* 3.7 5.4 - - - +
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Residues in contact with GLY 82 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B ARG 3.1 13.9 - - - -
17B TYR* 4.1 2.2 - - - -
57B GLU* 3.2 8.0 + - - -
58B VAL 2.8 36.2 + - - +
81B GLY* 1.3 74.5 - - - -
83B ILE* 1.3 60.3 + - - -
84B PHE* 3.3 12.9 - - - -
106B LEU* 3.8 13.0 - - - -
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Residues in contact with ILE 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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29A PRO* 4.3 9.9 - - + +
32A PHE* 5.5 0.4 - - + -
14B GLN* 3.0 38.9 + - + -
15B ARG* 2.9 25.0 + - + +
17B TYR* 3.5 32.8 - - + +
51B LEU* 3.8 14.6 - - + -
55B VAL* 3.6 24.0 - - + -
56B TYR 3.3 16.4 - - - +
57B GLU* 3.8 9.2 - - + +
82B GLY* 1.3 71.2 - - - -
84B PHE* 1.3 62.6 + - - +
304E PRO* 3.6 27.8 - - + +
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Residues in contact with PHE 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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11B PHE* 3.4 28.3 - + + -
12B GLN 3.3 9.2 - - - +
13B ILE* 3.8 26.2 - - + -
14B GLN* 4.1 3.4 - - - -
15B ARG 4.6 1.8 - - - -
16B ILE* 4.9 0.2 - - + -
56B TYR* 3.0 35.0 + - - +
58B VAL* 4.2 17.3 - - + -
82B GLY* 3.3 32.3 - - - -
83B ILE* 1.3 76.2 - - - +
85B SER* 1.3 60.0 + - - +
86B ILE* 3.5 23.4 + - + +
102B CYS* 3.9 24.5 - - + -
105B ILE* 4.2 11.2 - - + -
106B LEU* 3.8 33.0 - - + -
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Residues in contact with SER 85 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10B THR* 4.3 5.5 - - - +
11B PHE* 3.7 2.6 + - - -
12B GLN* 2.9 55.9 + - - +
14B GLN* 3.2 28.1 + - - +
54B ASP* 3.1 15.7 - - - -
55B VAL* 3.8 14.8 - - - +
84B PHE* 1.3 68.0 - - - +
86B ILE* 1.3 60.3 + - - +
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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