Contacts of the strand formed by residues 34 - 43 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4A GLU 6.2 0.2 - - - -
5A CYS 2.8 15.1 + - - +
6A ARG* 3.2 39.0 + - + +
7A VAL* 2.9 25.5 + - - +
32A GLY 3.8 1.8 + - - +
33A PHE* 1.3 70.3 - - - +
35A VAL* 1.3 61.5 + - - +
18E TYR* 2.5 45.8 + - - -
291E LEU 5.4 1.1 - - - +
292E ARG* 4.9 1.0 + - - -
293E MET 5.4 0.2 + - - -
294E VAL* 3.6 9.9 - - - +
295E GLN* 3.1 30.2 + - - +
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Residues in contact with VAL 35 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7A VAL* 3.5 9.4 - - + +
9A SER* 4.2 16.4 - - - -
25A THR* 4.3 23.6 - - + +
28A LEU* 3.8 36.1 - - + -
29A GLN* 4.1 15.3 - - + +
33A PHE* 3.5 10.4 + - + +
34A GLU* 1.3 79.9 + - - +
36A ASP* 1.3 75.8 + - - +
37A ALA* 4.3 4.5 - - + +
18E TYR* 4.0 3.1 + - - -
22E ARG* 2.6 35.9 + - - +
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Residues in contact with ASP 36 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6A ARG* 2.6 31.2 + - - -
7A VAL 2.9 7.6 + - - +
8A LEU* 3.4 7.3 - - + +
9A SER 2.8 28.8 + - - +
35A VAL* 1.3 77.0 - - - +
37A ALA* 1.3 61.0 + - - +
69A LEU* 4.6 0.3 - - - +
74A VAL 4.5 1.4 - - - +
77A TYR* 2.8 47.3 + - + +
15E VAL* 3.3 8.7 - - + +
16E ARG* 3.4 33.0 + - - +
17E GLY 4.5 0.7 + - - -
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Residues in contact with ALA 37 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9A SER 3.5 4.3 - - - -
21A ASN* 4.3 20.9 - - + +
25A THR* 4.8 5.2 - - + +
35A VAL* 4.7 5.8 - - + -
36A ASP* 1.3 73.6 - - - +
38A VAL* 1.3 61.0 + - - +
39A ASN* 4.0 1.8 - - - +
13E HIS* 3.3 23.2 + - + -
15E VAL* 2.9 34.8 + - - +
22E ARG* 3.6 18.9 - - - +
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Residues in contact with VAL 38 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8A LEU* 4.1 14.4 - - + -
9A SER 2.9 9.7 + - - +
10A ILE* 3.4 19.8 - - + -
11A GLN 3.1 14.7 + - - +
21A ASN* 2.8 15.0 - - - +
37A ALA* 1.3 72.5 - - - +
39A ASN* 1.3 68.0 + - - +
40A SER 3.6 0.2 + - - -
57A LEU* 5.0 0.2 - - + -
62A LEU* 3.9 22.9 - - + -
65A LEU* 3.9 24.5 - - + -
69A LEU* 5.3 2.9 - - + -
90A PHE* 4.4 4.0 - - + -
15E VAL* 3.4 31.0 - - + -
42E GLN* 3.5 3.1 - - - +
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Residues in contact with ASN 39 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11A GLN 3.1 4.0 - - - +
13A HIS* 3.5 32.9 + - + +
21A ASN* 3.1 30.0 - - - +
37A ALA* 4.6 0.5 - - - +
38A VAL* 1.3 73.5 - - - +
40A SER* 1.3 60.5 + - - +
41A VAL 3.1 4.2 + - - +
42A GLN* 5.9 1.6 - - + -
57A LEU* 3.0 26.0 - - - +
13E HIS* 3.2 42.5 + - - -
39E ASN* 4.0 8.3 - - - +
42E GLN* 2.7 22.3 - - - +
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Residues in contact with SER 40 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10A ILE* 5.0 0.2 - - - -
11A GLN* 2.9 22.2 + - - -
12A SER* 3.0 3.8 + - - -
38A VAL 3.6 2.8 + - - -
39A ASN* 1.3 72.2 - - - +
41A VAL* 1.3 71.1 + - - +
56A VAL* 3.9 1.2 - - - +
57A LEU* 3.0 27.0 + - - +
84A TYR 2.7 27.8 + - - -
85A THR* 4.4 3.9 - - - +
90A PHE* 3.6 38.0 - - - -
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Residues in contact with VAL 41 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12A SER* 3.2 30.5 - - - -
13A HIS* 2.8 33.1 + - - +
39A ASN* 3.1 6.4 - - - +
40A SER* 1.3 93.1 + - - +
42A GLN* 1.3 60.3 + - - +
43A PHE* 3.5 30.1 - - + -
55A GLN 3.3 11.2 - - - +
56A VAL* 3.6 23.3 - - + +
57A LEU* 4.4 2.9 - - - -
84A TYR* 4.2 11.2 - - + -
86A ARG* 5.2 6.3 - - - +
401A PLP 4.7 0.2 - - + -
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Residues in contact with GLN 42 (chain A).
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 26.2 - - + -
15A VAL* 3.8 6.5 - - - +
39A ASN* 5.9 1.6 - - + -
41A VAL* 1.3 73.1 - - - +
43A PHE* 1.3 64.4 + - - +
54A GLY* 3.1 3.6 - - - -
55A GLN* 2.8 54.9 + - + +
57A LEU* 5.5 0.8 - - + +
38E VAL* 3.7 7.3 - - - +
39E ASN* 3.1 46.7 - - - +
57E LEU* 3.8 5.4 - - - +
65E LEU* 3.6 26.8 - - + +
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Residues in contact with PHE 43 (chain A).
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 2.9 9.8 + - - +
14A VAL* 3.3 2.4 - - + -
15A VAL* 2.9 29.1 + - - +
41A VAL* 3.5 22.0 - - + -
42A GLN* 1.3 83.8 - - - +
44A SER* 1.3 63.0 + - - +
45A ASN 3.3 20.2 - - - +
47A THR* 4.5 4.3 - - + -
52A TRP* 3.4 42.6 - + + -
53A LYS 3.2 8.1 - - - +
54A GLY* 3.7 8.5 - - - -
55A GLN 3.1 25.8 - - - -
56A VAL* 4.0 6.1 - - + -
84A TYR* 4.1 24.2 - + - -
86A ARG* 4.1 10.5 - - - -
401A PLP 4.3 13.5 - - + -
65E LEU* 3.8 4.5 - - - -
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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