Contacts of the strand formed by residues 34 - 43 (chain E) in PDB entry 1RFU
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 34 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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18A TYR* 2.8 40.2 + - - -
291A LEU 5.6 0.9 - - - +
292A ARG* 5.0 2.6 + - - -
293A MET 5.9 0.2 + - - -
294A VAL* 4.3 5.3 - - - +
295A GLN* 3.4 27.0 + - - +
4E GLU* 6.1 0.4 - - - -
5E CYS 2.8 16.0 + - - +
6E ARG* 3.2 42.4 + - + +
7E VAL* 2.8 26.2 + - - +
32E GLY 3.8 1.4 + - - -
33E PHE* 1.3 70.5 - - - +
35E VAL* 1.3 65.9 + - - +
36E ASP* 5.1 0.2 - - - +
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Residues in contact with VAL 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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18A TYR* 4.2 3.3 + - - -
22A ARG* 3.0 23.5 + - - +
7E VAL* 3.6 9.4 - - + +
9E SER* 4.4 14.4 - - - -
25E THR* 4.0 25.8 - - + +
28E LEU* 3.8 36.1 - - + -
29E GLN* 4.2 14.8 - - + +
33E PHE* 3.6 10.4 + - + +
34E GLU* 1.3 82.8 + - - +
36E ASP* 1.3 85.2 + - - +
37E ALA* 4.2 4.5 - - + +
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Residues in contact with ASP 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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15A VAL* 3.4 9.2 - - + +
16A ARG* 3.7 31.8 + - - +
17A GLY 4.6 0.5 + - - -
22A ARG* 4.5 0.7 + - - -
6E ARG* 3.0 28.1 + - - -
7E VAL 2.8 9.3 + - - +
8E LEU* 3.4 8.2 - - + +
9E SER 2.8 27.0 + - - +
34E GLU* 5.1 0.2 - - - +
35E VAL* 1.3 82.5 - - - +
37E ALA* 1.3 60.1 + - - +
69E LEU* 4.7 0.2 - - - +
74E VAL 4.7 0.9 - - - +
77E TYR* 2.9 46.4 + - + +
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Residues in contact with ALA 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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13A HIS* 3.3 21.8 + - + -
15A VAL* 3.1 30.3 + - - +
22A ARG* 3.6 17.1 - - - +
9E SER 3.5 3.6 - - - -
21E ASN* 4.2 20.4 - - + +
25E THR* 4.8 7.2 - - + +
35E VAL* 4.6 6.1 - - + -
36E ASP* 1.3 74.0 - - - +
38E VAL* 1.3 63.4 + - - +
39E ASN* 4.1 2.9 - - - +
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Residues in contact with VAL 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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15A VAL* 3.5 29.4 - - + -
42A GLN* 3.7 2.5 - - - +
8E LEU* 4.0 16.8 - - + -
9E SER 2.9 6.3 + - - -
10E ILE* 3.4 22.7 - - + -
11E GLN 3.0 14.0 + - - +
21E ASN* 2.9 15.6 - - - +
37E ALA* 1.3 72.7 - - - +
39E ASN* 1.3 63.5 - - - +
40E SER 3.5 0.7 + - - -
57E LEU* 5.1 0.4 - - + -
62E LEU* 3.8 29.4 - - + -
65E LEU* 4.0 17.5 - - + -
69E LEU* 5.4 2.7 - - + -
90E PHE* 4.4 7.6 - - + -
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Residues in contact with ASN 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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13A HIS* 3.2 43.6 + - - -
39A ASN* 4.0 12.1 - - - +
42A GLN* 3.1 19.0 - - - +
11E GLN 3.0 3.1 - - - +
13E HIS* 3.5 32.7 + - + +
21E ASN* 3.4 24.9 - - - +
37E ALA* 4.6 1.4 - - - +
38E VAL* 1.3 73.1 - - - +
40E SER* 1.3 63.3 + - - +
41E VAL* 3.0 8.9 + - - +
42E GLN* 5.7 2.2 - - + -
57E LEU* 3.0 20.6 - - - +
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Residues in contact with SER 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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10E ILE* 4.9 0.2 - - - -
11E GLN* 2.8 22.9 + - - -
12E SER* 2.9 3.6 + - - -
38E VAL 3.5 3.0 + - - -
39E ASN* 1.3 71.6 - - - +
41E VAL* 1.3 70.8 + - - +
56E VAL* 3.9 1.4 - - - +
57E LEU* 3.1 26.2 + - - +
84E TYR 2.6 28.3 + - - -
85E THR* 4.3 4.3 - - - +
90E PHE* 3.6 38.1 - - - -
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Residues in contact with VAL 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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12E SER* 3.2 31.4 - - - +
13E HIS* 2.8 33.2 + - - +
39E ASN* 3.0 7.0 - - - +
40E SER* 1.3 96.8 - - - +
42E GLN* 1.3 60.2 + - - +
43E PHE* 3.6 28.0 - - + -
55E GLN 3.4 10.5 - - - +
56E VAL* 3.8 20.6 - - + +
57E LEU* 4.4 2.9 - - - -
84E TYR* 4.1 12.8 - - + +
85E THR* 6.0 0.2 - - + -
86E ARG* 5.2 6.7 - - + +
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Residues in contact with GLN 42 (chain E).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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37A ALA 3.9 5.5 + - - -
38A VAL* 3.5 10.5 - - - +
39A ASN* 2.7 59.7 - - - +
57A LEU* 3.8 4.0 - - - +
65A LEU* 3.6 19.4 - - + +
13E HIS* 3.1 17.1 - - + -
15E VAL* 4.0 3.8 - - + +
39E ASN* 5.7 2.2 - - + -
41E VAL* 1.3 75.2 - - - +
43E PHE* 1.3 63.0 + - - +
54E GLY* 3.1 2.9 - - - -
55E GLN* 2.8 54.9 + - + +
57E LEU* 5.4 1.5 - - + +
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Residues in contact with PHE 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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65A LEU* 3.9 4.9 - - - -
13E HIS 2.9 9.4 + - - +
14E VAL* 3.2 2.2 - - + -
15E VAL* 2.8 28.9 + - - +
41E VAL* 3.6 22.2 - - + -
42E GLN* 1.3 83.5 - - - +
44E SER* 1.3 62.2 + - - +
45E ASN 3.3 20.0 - - - +
47E THR* 4.6 4.0 - - + -
52E TRP* 3.2 45.1 - + + -
53E LYS 3.3 7.6 - - - +
54E GLY* 3.6 9.6 - - - -
55E GLN 3.3 20.9 - - - -
56E VAL* 3.9 14.1 - - + -
84E TYR* 4.1 23.1 - + - -
86E ARG* 4.1 6.7 - - - -
4401E PLP 4.1 13.2 - - + -
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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