Contacts of the strand formed by residues 66 - 76 (chain B) in PDB entry 3E0D
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 LYS 66 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39B ASP 5.7 0.4 - - - +
40B PRO 2.9 18.0 + - - +
41B ALA* 3.3 9.8 - - + +
42B LEU 3.1 24.9 + - - -
64B GLY 4.0 1.4 + - - -
65B VAL* 1.3 72.5 - - - +
67B PRO* 1.3 72.4 - - + +
68B ILE* 4.4 1.9 - - + +
278B ALA 3.0 19.5 + - - +
279B ARG* 2.9 30.2 + - - +
281B CYS 3.4 24.3 + - - -
282B ASP* 4.2 7.7 - - - +
283B VAL 5.6 0.4 - - - +
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Residues in contact with PRO 67 (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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42B LEU 3.6 4.9 - - - +
56B PHE* 3.6 25.6 - - + -
57B TYR* 3.7 43.3 - - + +
60B ALA* 4.0 11.7 - - + -
61B THR* 4.8 7.2 - - - +
65B VAL* 3.3 10.5 - - + +
66B LYS* 1.3 93.3 - - + +
68B ILE* 1.3 66.1 + - - +
69B ILE* 4.2 2.2 - - + -
281B CYS 4.8 5.2 - - - +
283B VAL* 5.3 7.2 - - - +
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Residues in contact with ILE 68 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10B LEU* 3.8 16.2 - - + -
41B ALA* 4.1 13.5 - - + -
42B LEU 2.8 17.9 + - - +
43B ALA* 3.1 12.1 - - + -
44B MET* 2.8 31.0 + - - +
56B PHE* 3.9 1.5 - - - -
66B LYS* 4.4 3.4 - - + +
67B PRO* 1.3 80.3 - - - +
69B ILE* 1.3 69.3 + - - +
70B GLY 3.4 0.2 + - - -
99B LEU* 4.4 12.8 - - + -
100B ALA 4.3 7.9 - - - +
278B ALA* 3.7 37.7 - - + +
281B CYS* 4.2 33.0 - - + +
283B VAL* 6.3 1.6 - - - -
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Residues in contact with ILE 69 (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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44B MET* 4.3 5.4 - - + -
50B LEU* 4.4 11.7 - - + -
53B ALA* 4.4 29.6 - - + +
56B PHE* 5.2 7.2 - - + -
57B TYR* 4.7 9.9 - - + -
67B PRO* 5.6 2.0 - - + -
68B ILE* 1.3 74.4 - - - +
70B GLY* 1.3 61.1 + - - +
99B LEU* 4.0 0.5 - - - -
100B ALA* 3.1 31.8 + - + +
106B TYR* 4.0 32.1 - - + -
109B LEU* 3.5 18.3 - - + +
283B VAL* 4.2 21.1 - - + +
285B LEU* 4.2 22.7 - - + -
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Residues in contact with GLY 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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44B MET* 2.7 34.6 + - - +
45B THR* 3.7 10.3 - - - -
46B ASP 4.3 1.2 + - - -
49B ASN 4.7 0.5 - - - +
50B LEU* 3.7 14.9 - - - +
68B ILE 3.4 1.6 + - - -
69B ILE* 1.3 75.0 - - - +
71B TYR* 1.3 63.0 + - - +
98B LEU 3.2 14.1 - - - -
99B LEU* 4.2 4.0 - - - -
109B LEU* 4.2 3.1 - - - -
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Residues in contact with TYR 71 (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 THR* 3.9 6.6 - - - +
46B ASP 4.1 2.9 - - - -
48B GLY* 3.4 17.2 + - - -
49B ASN* 3.1 38.1 - - - -
50B LEU* 3.9 9.2 - - + -
70B GLY* 1.3 75.8 - - - +
72B GLU* 1.3 58.4 + - - +
73B ALA* 3.4 37.6 + - + -
74B TYR 5.3 0.2 + - - -
96B LEU 3.4 2.4 - - - +
98B LEU* 2.9 43.9 + - + +
109B LEU* 3.8 24.0 - - + -
112B LEU* 5.0 2.5 - - + -
113B ALA* 3.6 32.0 + - + -
116B ALA* 3.5 26.7 - - - +
125B PRO 4.5 1.9 + - - -
127B ILE* 4.6 8.4 - - + +
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Residues in contact with GLU 72 (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 HIS* 2.9 19.7 + - + +
13B HIS* 2.8 35.3 + - - -
45B THR* 4.1 10.0 - - - +
46B ASP 2.9 21.1 + - - +
47B HIS* 3.4 10.7 + - - +
48B GLY 2.9 25.2 + - - -
71B TYR* 1.3 69.0 - - - +
73B ALA* 1.3 61.3 + - - +
74B TYR* 3.7 2.1 + - + -
95B HIS* 2.8 41.5 + - + +
96B LEU 3.3 13.9 + - - +
97B THR* 4.6 3.0 + - - +
145B CYS* 3.2 15.6 + - - -
212B ASN* 4.2 0.7 + - - +
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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
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71B TYR* 3.4 33.3 + - + -
72B GLU* 1.3 73.5 - - - +
74B TYR* 1.3 62.4 + - - +
75B VAL* 3.6 1.2 + - + -
94B PHE 3.4 0.7 - - - +
95B HIS* 3.4 6.8 - - - -
96B LEU* 2.8 43.3 + - + +
98B LEU* 4.1 6.5 - - + -
127B ILE* 3.7 26.7 - - + -
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Residues in contact with TYR 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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47B HIS* 3.4 46.9 + - + +
48B GLY* 4.0 9.6 - - - -
71B TYR* 5.3 0.2 + - - -
72B GLU* 4.9 1.1 - - + -
73B ALA* 1.3 73.3 - - - +
75B VAL* 1.3 58.4 + - - +
93B TYR* 3.5 32.3 - + + -
94B PHE 3.3 2.7 - - - +
95B HIS* 3.7 27.5 + + - -
124B LYS* 3.1 45.3 - - + -
125B PRO* 3.5 25.7 + - + +
126B ARG* 3.2 16.0 - - + -
127B ILE* 2.9 27.7 + - - +
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Residues in contact with VAL 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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73B ALA* 3.9 3.6 - - + +
74B TYR* 1.3 74.7 - - - +
76B ALA* 1.3 72.3 + - - +
93B TYR* 3.2 2.3 - - - -
94B PHE* 2.7 49.5 + - + +
95B HIS 4.0 0.2 - - - -
96B LEU* 3.7 34.1 - - + -
127B ILE* 3.5 17.5 - - + +
128B ASP 5.4 0.9 - - - -
129B ARG* 4.4 17.0 - - + +
132B LEU* 5.9 2.0 - - + -
149B GLU* 3.5 31.4 - - - +
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Residues in contact with ALA 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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74B TYR 4.1 1.2 + - - -
75B VAL* 1.3 79.7 - - - +
77B ALA* 1.3 67.2 + - - +
78B GLU 3.2 5.0 + - - +
79B SER 3.7 24.5 - - - +
80B ARG* 4.2 1.6 - - - +
82B ASP* 5.4 0.2 - - - +
92B GLY 3.9 6.5 - - - -
93B TYR* 4.3 3.4 - - - +
126B ARG* 3.5 30.8 - - + +
127B ILE 3.0 18.8 + - - +
128B ASP* 4.2 1.1 - - - +
129B ARG* 3.5 10.9 + - - -
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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