Contacts of the strand formed by residues 81 - 90 (chain B) in PDB entry 2E3V
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 THR 81 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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49B ALA* 3.4 4.7 - - - -
50B VAL* 2.8 49.1 + - + +
80B THR* 1.3 75.1 - - - +
82B TYR* 1.3 57.8 + - - +
102B GLU* 3.7 31.0 + - + +
103B PHE 3.3 12.6 - - - +
104B LYS* 3.7 23.1 - - + +
1006B PGE 3.8 12.1 - - - +
1007B PGE 4.9 0.6 - - - -
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Residues in contact with TYR 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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47B TRP* 3.9 17.7 - + + -
48B ARG 3.4 7.2 - - - -
49B ALA* 3.4 29.8 - - + -
52B GLU* 4.5 3.1 - - - -
56B HIS* 5.7 1.1 - + - -
76B LEU* 3.6 25.8 - - + -
77B LYS* 2.8 46.7 + - - +
80B THR* 3.3 40.6 - - + -
81B THR* 1.3 73.0 - - - +
83B ALA* 1.3 61.4 + - - +
101B SER 3.8 0.3 - - - +
102B GLU* 3.3 0.2 - - - -
103B PHE* 2.8 66.1 + + + +
105B THR* 4.0 1.8 - - + -
1006B PGE 3.3 12.1 - - - -
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Residues in contact with ALA 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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47B TRP* 3.1 6.9 - - - +
48B ARG 2.9 33.5 + - - +
55B TRP* 3.6 15.5 - - + -
82B TYR* 1.3 72.8 - - - +
84B VAL* 1.3 60.0 + - - +
100B ALA* 4.0 2.5 - - + -
101B SER 3.3 6.3 - - - -
1006B PGE 3.3 51.9 - - - +
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Residues in contact with VAL 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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15B ILE* 3.4 16.0 - - + +
18B VAL* 4.5 3.4 - - + -
27B VAL* 4.3 24.2 - - + -
45B ALA* 4.9 0.2 - - + -
46B GLU 3.2 12.6 - - - +
47B TRP* 4.2 8.5 - - + -
73B ILE* 4.3 14.4 - - + -
83B ALA* 1.3 74.4 - - - +
85B ARG* 1.3 69.1 + - - +
86B LEU* 4.4 8.3 - - + -
100B ALA* 3.2 3.0 - - - -
101B SER* 2.7 50.1 + - - +
103B PHE* 3.7 27.6 - - + -
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Residues in contact with ARG 85 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B ILE* 4.1 2.2 - - - -
45B ALA* 3.5 2.6 - - - -
46B GLU* 2.7 68.6 + - + +
55B TRP* 3.5 54.9 - - + +
84B VAL* 1.3 76.9 - - - +
86B LEU* 1.3 65.7 + - - +
97B ILE* 3.4 27.6 - - + +
98B SER* 3.4 27.1 - - - +
99B ALA 3.8 3.4 - - - +
100B ALA* 4.0 6.5 - - - +
1006B PGE 6.0 0.2 - - - -
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Residues in contact with LEU 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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13B PRO* 3.5 20.4 - - + +
15B ILE* 3.8 20.4 - - + -
27B VAL* 4.1 11.4 - - + -
29B PHE* 3.6 46.2 - - + -
43B TYR* 5.8 4.3 - - + -
44B LYS 3.3 5.2 - - - +
45B ALA* 3.5 25.1 - - + -
71B VAL* 3.9 14.4 - - + -
84B VAL* 4.4 4.7 - - + -
85B ARG* 1.3 84.1 - - - +
87B ALA* 1.3 61.4 + - - +
97B ILE* 3.7 3.1 - - - -
98B SER* 2.7 40.4 + - - +
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Residues in contact with ALA 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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13B PRO* 3.7 7.6 - - - -
43B TYR* 3.3 8.3 - - - +
44B LYS* 2.8 33.5 + - + +
86B LEU* 1.3 75.2 - - - +
88B ALA* 1.3 61.1 + - - +
94B LEU* 3.8 18.2 - - + -
95B GLY 3.8 20.2 - - - +
96B GLU 3.9 5.8 - - - +
97B ILE* 3.6 18.4 - - + -
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Residues in contact with ALA 88 (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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10B PRO* 3.4 20.5 - - + +
11B SER 4.1 5.0 + - - +
13B PRO* 3.9 3.1 - - + +
31B GLU* 3.8 18.6 - - - +
40B ILE* 4.0 6.7 - - + -
42B LYS 3.6 3.8 - - - -
43B TYR* 3.8 23.1 - - + -
87B ALA* 1.3 75.4 - - - +
89B LEU* 1.3 61.0 + - - +
94B LEU* 3.5 3.9 - - - +
95B GLY* 2.8 27.5 + - - +
96B GLU 4.9 1.4 + - - -
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Residues in contact with LEU 89 (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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16A ASP* 5.8 2.9 - - + +
10B PRO* 4.2 2.5 - - - -
40B ILE* 3.6 3.1 - - - -
41B LEU* 2.7 33.1 + - + -
42B LYS* 2.7 41.2 + - + +
59B TRP* 4.1 20.4 - - + -
88B ALA* 1.3 75.5 - - - +
90B ASN* 1.3 60.9 + - - +
93B GLY* 3.6 5.8 - - - -
94B LEU* 3.5 35.0 - - + +
1005B PEG 3.7 36.3 - - - +
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Residues in contact with ASN 90 (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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9B GLY 4.3 1.6 - - - -
10B PRO* 3.5 32.0 - - + +
38B VAL* 3.4 25.0 + - + +
39B PRO 3.3 24.2 - - - +
40B ILE* 4.4 2.8 - - + +
41B LEU* 3.8 9.0 - - - -
89B LEU* 1.3 74.7 - - - +
91B GLY* 1.3 63.5 + - - +
92B LYS* 2.9 20.8 + - - +
93B GLY* 3.1 27.2 + - - +
1005B PEG 3.1 15.4 + - - -
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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