Contacts of the strand formed by residues 34 - 43 (chain G) 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 G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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18D TYR* 2.9 39.8 + - - -
291D LEU 5.8 0.2 - - - +
292D ARG* 4.9 2.9 + - - -
294D VAL* 4.4 5.3 - - - +
295D GLN* 3.5 24.8 + - - +
5G CYS 2.7 19.5 + - - +
6G ARG* 3.2 41.0 + - + +
7G VAL* 2.8 26.7 + - - +
32G GLY 3.7 1.4 + - - +
33G PHE* 1.3 72.7 - - - +
35G VAL* 1.3 64.3 + - - +
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Residues in contact with VAL 35 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18D TYR* 4.4 2.8 + - - -
22D ARG* 3.1 26.6 + - - +
7G VAL* 3.6 10.3 - - + +
9G SER* 4.3 15.7 - - - -
25G THR* 4.0 26.0 - - + +
28G LEU* 3.8 35.7 - - + -
29G GLN* 4.0 15.0 - - + +
33G PHE* 3.6 9.3 + - + +
34G GLU* 1.3 83.2 + - - +
36G ASP* 1.3 80.3 + - - +
37G ALA* 4.0 5.4 - - + +
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Residues in contact with ASP 36 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15D VAL* 3.5 9.0 - - + +
16D ARG* 3.9 29.9 + - - +
17D GLY 4.9 0.9 + - - -
6G ARG* 2.9 29.8 + - - -
7G VAL 2.8 9.1 + - - +
8G LEU* 3.4 9.0 - - + +
9G SER 2.9 26.9 + - - +
34G GLU* 5.4 0.2 - - - +
35G VAL* 1.3 79.8 - - - +
37G ALA* 1.3 59.5 + - - +
69G LEU* 4.8 0.9 - - - +
74G VAL 4.6 1.6 - - - +
77G TYR* 2.9 46.0 + - + +
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Residues in contact with ALA 37 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13D HIS* 3.4 21.0 + - + -
15D VAL* 3.2 32.2 + - - +
22D ARG* 3.8 18.0 - - - +
9G SER 3.5 5.6 - - - +
21G ASN* 4.4 17.3 - - + +
25G THR* 4.7 7.6 - - + +
35G VAL* 4.6 6.5 - - + -
36G ASP* 1.3 72.9 - - - +
38G VAL* 1.3 63.5 + - - +
39G ASN* 4.0 2.5 - - - +
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Residues in contact with VAL 38 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15D VAL* 3.7 22.7 - - + -
42D GLN* 3.8 2.9 - - - +
8G LEU* 4.1 17.7 - - + -
9G SER 3.0 9.3 + - - +
10G ILE* 3.4 18.5 - - + -
11G GLN 3.1 14.0 + - - -
21G ASN* 3.0 13.7 - - - +
37G ALA* 1.3 75.8 - - - +
39G ASN* 1.3 68.5 + - - +
40G SER 3.5 0.3 + - - -
57G LEU* 5.0 0.2 - - + -
62G LEU* 3.8 29.6 - - + -
65G LEU* 3.9 19.3 - - + -
69G LEU* 5.4 3.4 - - + -
90G PHE* 4.4 4.7 - - + -
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Residues in contact with ASN 39 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13D HIS* 3.1 42.6 + - - -
39D ASN* 4.0 6.3 - - - +
42D GLN* 3.1 17.2 - - - +
11G GLN 3.1 3.8 - - - -
13G HIS* 3.5 35.5 + - + +
21G ASN* 3.3 29.5 - - - +
37G ALA* 4.6 1.9 - - - +
38G VAL* 1.3 74.2 - - - +
40G SER* 1.3 64.6 + - - +
41G VAL* 3.0 5.0 + - - +
42G GLN* 5.7 1.8 - - + -
57G LEU* 3.0 23.6 - - - +
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Residues in contact with SER 40 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10G ILE* 4.8 0.4 - - - -
11G GLN* 2.8 21.5 + - - -
12G SER* 3.0 3.8 + - - -
38G VAL 3.5 3.0 + - - -
39G ASN* 1.3 71.4 - - - +
41G VAL* 1.3 71.1 + - - +
56G VAL* 3.8 1.7 - - - +
57G LEU* 3.1 26.1 + - - +
84G TYR 2.6 29.6 + - - -
85G THR* 4.5 3.6 - - - -
90G PHE* 3.6 37.3 - - - -
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Residues in contact with VAL 41 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12G SER* 3.2 30.7 - - - +
13G HIS* 2.8 34.3 + - - +
39G ASN* 3.0 6.9 - - - +
40G SER* 1.3 97.1 - - - +
42G GLN* 1.3 60.5 + - - +
43G PHE* 3.6 30.7 - - + -
55G GLN 3.4 10.8 - - - +
56G VAL* 3.7 21.5 - - + +
57G LEU* 4.4 3.1 - - - -
84G TYR* 4.2 12.8 - - + +
85G THR* 5.3 0.4 - - + -
86G ARG* 5.2 5.8 - - + +
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Residues in contact with GLN 42 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37D ALA 4.0 2.6 + - - -
38D VAL* 3.6 10.3 - - - +
39D ASN* 3.0 51.6 - - - +
57D LEU* 4.0 4.7 - - - +
65D LEU* 3.7 23.1 - - + +
13G HIS* 3.2 21.4 - - + -
15G VAL* 3.9 5.7 - - - +
39G ASN* 5.7 2.0 - - + -
41G VAL* 1.3 75.4 - - - +
43G PHE* 1.3 64.6 + - - +
54G GLY* 3.1 3.5 - - - -
55G GLN* 2.9 52.1 + - + +
57G LEU* 5.4 1.3 - - + +
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Residues in contact with PHE 43 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65D LEU* 4.1 4.0 - - - -
13G HIS 2.9 9.2 + - - +
14G VAL* 3.2 2.1 - - + -
15G VAL* 2.8 35.7 + - - +
41G VAL* 3.6 22.9 - - + -
42G GLN* 1.3 84.0 - - - +
44G SER* 1.3 56.1 + - - +
45G ASN 3.2 17.7 - - - +
47G THR* 4.5 4.0 - - + -
52G TRP* 3.3 42.2 - + + -
53G LYS 3.3 7.6 - - - +
54G GLY* 3.8 9.0 - - - -
55G GLN 3.3 20.9 - - - -
56G VAL* 3.9 9.4 - - + -
84G TYR* 4.2 23.6 - + - -
86G ARG* 4.0 11.4 - - - -
6401G PLP 4.0 17.0 - - + -
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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