Contacts of the strand formed by residues 34 - 43 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4B GLU 6.1 0.2 - - - -
5B CYS 2.8 16.7 + - - +
6B ARG* 3.1 44.9 + - + +
7B VAL 2.9 23.9 + - - -
32B GLY 3.9 1.0 + - - -
33B PHE* 1.3 70.9 - - - +
35B VAL* 1.3 63.3 + - - +
17F GLY 5.5 0.3 + - - -
18F TYR* 2.5 47.4 + - - -
22F ARG* 4.3 0.2 + - - -
291F LEU 4.9 3.4 - - - +
292F ARG* 5.2 1.2 + - - -
294F VAL* 3.9 6.7 - - - +
295F GLN* 3.5 27.2 + - - +
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Residues in contact with VAL 35 (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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7B VAL* 3.5 10.8 - - + +
9B SER* 4.3 15.9 - - - -
25B THR* 4.3 24.5 - - + +
28B LEU* 3.8 35.2 - - + -
29B GLN* 4.1 14.4 - - + -
33B PHE* 3.7 10.2 + - + +
34B GLU* 1.3 79.5 + - - +
36B ASP* 1.3 76.0 + - - +
37B ALA* 4.2 4.0 - - + +
18F TYR* 3.9 4.2 + - - +
22F ARG* 2.4 36.1 + - - +
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Residues in contact with ASP 36 (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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6B ARG* 2.7 28.7 + - - -
7B VAL 2.8 8.4 + - - +
8B LEU* 3.3 8.6 - - + +
9B SER 2.8 27.4 + - - +
34B GLU 4.1 0.2 + - - -
35B VAL* 1.3 76.1 - - - +
37B ALA* 1.3 59.4 + - - +
77B TYR* 2.6 48.5 + - + +
15F VAL* 3.0 9.6 - - + +
16F ARG* 3.0 33.2 + - - +
17F GLY 4.3 0.7 + - - -
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Residues in contact with ALA 37 (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 SER 3.5 3.8 - - - -
21B ASN* 4.2 20.6 - - + +
25B THR* 4.7 7.2 - - + +
35B VAL* 4.6 4.9 - - + -
36B ASP* 1.3 73.2 - - - +
38B VAL* 1.3 61.2 + - - +
39B ASN* 4.5 1.6 - - - +
13F HIS* 3.0 24.4 + - + -
15F VAL* 2.7 36.3 + - - +
22F ARG* 3.3 17.3 - - - +
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Residues in contact with VAL 38 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B LEU* 4.0 13.7 - - + -
9B SER 2.9 9.1 + - - +
10B ILE* 3.4 19.3 - - + -
11B GLN 3.1 15.2 + - - -
21B ASN* 2.9 14.3 - - - +
37B ALA* 1.3 72.7 - - - +
39B ASN* 1.3 66.2 + - - +
40B SER 3.6 0.2 + - - -
57B LEU* 5.0 1.1 - - + -
62B LEU* 3.8 22.4 - - + -
65B LEU* 3.8 25.6 - - + -
69B LEU* 5.4 2.2 - - + -
90B PHE* 4.5 4.0 - - + -
15F VAL* 3.2 32.5 - - + -
42F GLN* 3.4 2.9 - - - +
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Residues in contact with ASN 39 (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 GLN 3.1 3.6 - - - +
13B HIS* 3.5 27.2 + - + +
21B ASN* 3.1 30.0 - - - +
37B ALA* 4.5 0.9 - - - +
38B VAL* 1.3 74.6 - - - +
40B SER* 1.3 59.0 + - - +
41B VAL 3.1 5.0 + - - +
42B GLN* 5.9 1.6 - - + -
57B LEU* 2.9 26.3 - - - +
13F HIS* 3.3 40.4 + - - -
39F ASN* 3.7 16.2 - - - +
42F GLN* 2.8 21.2 - - - +
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Residues in contact with SER 40 (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 ILE* 4.9 0.2 - - - -
11B GLN* 2.9 21.4 + - - -
12B SER* 3.0 3.6 + - - -
38B VAL 3.6 2.8 + - - -
39B ASN* 1.3 72.0 - - - +
41B VAL* 1.3 71.3 + - - +
56B VAL* 3.9 1.4 - - - +
57B LEU* 3.0 27.0 + - - +
84B TYR 2.6 29.3 + - - -
85B THR* 4.4 3.5 - - - +
90B PHE* 3.5 37.8 - - - -
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Residues in contact with VAL 41 (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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12B SER* 3.2 31.2 - - - +
13B HIS* 2.8 32.3 + - - +
39B ASN* 3.1 5.6 - - - +
40B SER* 1.3 94.9 - - - +
42B GLN* 1.3 61.6 + - - +
43B PHE* 3.4 36.6 - - + -
55B GLN 3.4 5.4 - - - +
56B VAL* 3.7 21.5 - - + +
57B LEU* 4.4 3.1 - - - -
84B TYR* 4.2 10.1 - - + +
85B THR* 6.2 0.2 - - + -
86B ARG* 5.2 6.3 - - - +
1401B PLP 4.8 0.2 - - + -
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Residues in contact with GLN 42 (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 HIS* 3.2 21.3 - - + -
15B VAL* 3.9 6.1 - - - +
39B ASN* 5.9 1.3 - - + -
41B VAL* 1.3 74.9 - - - +
43B PHE* 1.3 63.4 + - - +
54B GLY* 3.1 3.8 - - - -
55B GLN* 2.9 43.6 + - + +
57B LEU* 5.4 0.8 - - + +
37F ALA 4.1 2.6 + - - -
38F VAL* 3.6 10.7 - - - +
39F ASN* 3.1 49.2 - - - +
57F LEU* 3.8 13.3 - - - +
65F LEU* 3.7 27.3 - - + +
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Residues in contact with PHE 43 (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 HIS 2.9 8.6 + - - +
14B VAL* 3.2 2.8 - - + -
15B VAL* 2.8 28.2 + - - +
41B VAL* 3.4 24.5 - - + -
42B GLN* 1.3 83.2 - - - +
44B SER* 1.3 62.7 + - - +
45B ASN 3.2 17.9 - - - +
47B THR* 4.7 3.6 - - + -
52B TRP* 3.5 38.6 - + + -
53B LYS 3.3 7.9 - - - +
54B GLY* 3.8 8.7 - - - -
55B GLN 3.2 24.7 - - - -
56B VAL* 3.9 7.0 - - + -
84B TYR* 4.1 25.1 - + - -
86B ARG* 4.1 12.6 - - - -
1401B PLP 4.0 17.0 - - + -
65F LEU* 3.9 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