Contacts of the strand formed by residues 30 - 43 (chain E) in PDB entry 2BG9
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 VAL 30 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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28E ILE* 3.4 2.8 + - + -
29E ASP* 1.3 71.2 - - - +
31E THR* 1.3 55.6 + - - +
32E LEU* 3.3 21.1 - - + -
57E ILE* 5.6 1.6 - - + -
58E GLN 3.4 4.7 - - - +
59E TRP* 3.6 14.4 - - + -
85E TRP* 3.0 43.7 - - + -
87E PRO* 5.5 5.8 - - + -
156E ASN 2.7 26.2 + - - +
157E LEU* 2.9 26.0 - - + -
158E GLN* 2.6 39.3 + - - +
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Residues in contact with THR 31 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29E ASP 4.3 1.0 + - - -
30E VAL* 1.3 66.8 - - - +
32E LEU* 1.3 74.2 + - - +
33E LYS* 6.0 3.8 - - + -
58E GLN* 2.4 85.5 + - + +
59E TRP* 3.7 2.9 + - - -
60E ASN* 4.8 3.5 + - - -
158E GLN* 3.5 29.2 + - + +
159E LEU* 6.0 1.1 - - - +
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Residues in contact with LEU 32 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30E VAL* 3.3 17.7 - - + -
31E THR* 1.3 94.7 - - - +
33E LYS* 1.3 76.0 + - - +
55E ILE* 4.7 4.5 - - + -
56E GLU* 2.8 12.1 - - - +
57E ILE* 4.0 23.1 - - + -
58E GLN 4.2 0.4 - - - +
87E PRO* 4.7 12.3 - - + -
89E VAL* 5.4 2.5 - - + -
145E PHE* 4.2 12.1 - - + -
146E ARG* 5.4 1.6 - - - -
147E SER* 5.5 1.6 - - - +
157E LEU* 3.0 40.6 - - + -
158E GLN 3.2 22.7 + - - +
159E LEU* 3.3 5.2 - - - +
208E ILE* 3.4 19.7 - - + -
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Residues in contact with LYS 33 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31E THR* 6.0 4.0 - - + -
32E LEU* 1.3 86.0 - - - +
34E LEU* 1.3 66.7 + - - +
35E THR* 6.1 0.4 - - - +
54E TRP 3.2 0.5 - - - +
56E GLU* 2.6 66.3 + - + +
145E PHE* 5.2 2.1 - - - -
159E LEU* 4.4 17.7 - - + +
160E SER* 2.4 43.0 + - - +
210E PHE* 5.8 0.7 - - - -
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Residues in contact with LEU 34 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33E LYS* 1.3 77.8 - - - +
35E THR* 1.3 64.3 + - - +
36E LEU* 4.0 0.8 + - + +
53E VAL* 4.0 24.5 - - + -
54E TRP 3.0 24.0 - - - +
55E ILE* 3.3 23.8 - - + -
91E LEU* 4.8 0.9 - - + -
99E PHE* 6.2 0.2 - - + -
123E TYR* 4.7 8.3 - - - +
145E PHE* 3.2 41.3 - - + -
175E GLU* 4.0 5.0 - - - +
188E ARG* 4.9 3.5 + - - -
210E PHE* 2.9 48.9 - - + -
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Residues in contact with THR 35 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33E LYS* 6.1 0.3 - - - +
34E LEU* 1.3 75.8 + - - +
36E LEU* 1.3 65.6 + - - +
37E THR* 3.5 0.2 + - - -
53E VAL* 3.9 0.4 - - - -
54E TRP* 3.0 67.9 + - + +
56E GLU* 5.3 4.7 + - - +
175E GLU* 2.6 32.7 + - + +
176E ASP* 5.6 0.2 - - + -
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Residues in contact with LEU 36 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34E LEU* 4.0 1.6 - - - -
35E THR* 1.3 82.2 - - - +
37E THR* 1.3 62.2 + - - +
38E ASN 4.8 2.2 - - - +
39E LEU* 5.3 9.2 - - + -
51E THR* 2.9 44.0 - - + +
52E ASN 4.2 2.0 - - - -
53E VAL* 5.0 4.9 - - + +
54E TRP* 3.6 0.2 - - - -
173E ASP* 2.1 55.2 - - - +
175E GLU* 2.4 20.6 + - + +
176E ASP* 3.2 20.8 - - - +
177E PHE* 5.7 1.1 - - - -
188E ARG* 3.1 24.4 - - - +
210E PHE* 6.0 1.3 - - + -
212E LEU* 4.4 4.5 - - + -
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Residues in contact with THR 37 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93A TYR 5.7 4.9 - - - +
94A ASN* 6.3 2.5 - - - -
127A TYR* 5.9 1.0 - - - -
35E THR 3.5 1.0 + - - -
36E LEU* 1.3 70.4 - - - +
38E ASN* 1.3 67.0 + - + +
52E ASN* 3.1 23.4 + - + +
54E TRP* 2.6 60.2 - - + -
176E ASP* 3.4 31.4 - - - +
178E THR* 5.2 1.6 + - - -
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Residues in contact with ASN 38 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97A ASP* 5.8 1.8 + - - -
127A TYR* 3.0 40.9 + - + -
36E LEU* 4.9 1.3 - - - +
37E THR* 1.3 84.4 - - + +
39E LEU* 1.3 67.1 + - - +
40E ILE* 3.0 37.8 + - - +
51E THR* 2.6 41.4 - - - +
52E ASN* 2.7 27.0 + - + +
122E ILE* 5.5 0.6 - - - +
176E ASP 4.2 2.5 + - - -
178E THR* 4.1 5.7 + - - -
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Residues in contact with LEU 39 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36E LEU* 5.3 9.2 - - + -
38E ASN* 1.3 77.2 + - - +
40E ILE* 1.3 63.9 - - - +
41E SER 5.1 0.4 - - - +
42E LEU* 3.6 15.5 - - + -
49E LEU* 3.2 31.2 - - + -
50E THR 3.4 0.4 - - - -
51E THR* 3.1 22.7 - - + +
173E ASP* 5.8 2.9 - - - +
176E ASP 5.2 1.6 + - - +
177E PHE* 5.2 6.5 - - + -
178E THR* 3.9 26.2 + - - +
183E TRP* 2.9 52.3 - - + +
185E ILE* 5.7 5.6 - - + -
212E LEU* 6.0 4.3 - - + -
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Residues in contact with ILE 40 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97A ASP* 5.0 15.9 - - - +
127A TYR* 5.1 5.8 - - + +
38E ASN* 3.0 37.7 - - + +
39E LEU* 1.3 75.3 - - - +
41E SER* 1.3 59.9 + - - +
50E THR* 2.5 41.0 + - + +
51E THR 5.2 0.2 - - - +
52E ASN 5.2 0.4 - - - +
122E ILE* 4.2 22.0 - - + -
183E TRP* 6.2 1.3 - - - -
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Residues in contact with SER 41 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39E LEU 3.6 1.4 - - - -
40E ILE* 1.3 84.2 - - - +
42E LEU* 1.3 63.0 + - - +
43E ASN* 3.8 7.6 - - - -
48E ALA 3.4 1.7 - - - +
49E LEU* 2.9 26.9 - - - +
50E THR* 2.6 32.1 + - - -
124E ARG* 3.5 16.9 + - - -
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Residues in contact with LEU 42 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39E LEU* 3.6 26.9 - - + -
41E SER* 1.3 77.2 - - - +
43E ASN* 1.3 67.1 + - - +
44E GLU* 3.5 22.7 + - - +
48E ALA 4.8 0.7 - - - +
49E LEU* 4.0 14.8 - - + -
129E ILE* 5.8 0.2 - - + -
133E TYR* 5.9 1.8 - - + -
183E TRP* 3.1 60.1 - - + +
214E ILE* 5.6 2.0 - - + -
216E ARG* 3.8 20.7 + - - +
279E VAL* 4.9 8.5 - - - +
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Residues in contact with ASN 43 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41E SER* 3.8 7.9 + - - +
42E LEU* 1.3 77.9 - - - +
44E GLU* 1.3 58.6 + - - +
45E LYS* 3.5 11.8 - - + -
46E GLU* 3.3 12.7 + - + +
47E GLU 2.9 20.4 + - - -
48E ALA* 3.0 26.5 + - + +
124E ARG* 4.7 16.1 - - - +
129E ILE* 4.1 0.4 - - - -
278E ASN 3.5 20.8 - - - +
279E VAL* 5.1 1.4 - - - +
280E PRO* 5.7 0.7 - - - -
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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