Contacts of the helix formed by residues 20 - 31 (chain D) 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 GLY 20 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11D GLN* 3.7 17.4 - - - +
12D SER* 3.0 25.1 - - - -
19D VAL* 1.3 72.0 - - - +
21D ASN* 1.3 65.8 + - - -
22D ARG 3.0 2.7 - - - -
23D ALA* 3.0 11.4 + - - +
24D ALA* 3.1 12.3 + - - +
235D ASP* 3.8 18.5 + - - +
3401D PLP 4.0 0.6 - - - -
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Residues in contact with ASN 21 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9D SER* 2.7 40.7 + - - +
11D GLN* 3.3 14.1 + - - +
12D SER 2.6 12.5 + - - +
13D HIS* 5.2 2.5 - - + +
20D GLY* 1.3 71.5 - - - -
22D ARG* 1.3 56.4 + - - +
24D ALA* 4.3 4.5 - - - +
25D THR* 2.5 48.9 + - - +
37D ALA* 4.1 10.4 - - + +
38D VAL 2.8 28.8 + - - +
39D ASN* 3.1 20.5 - - - +
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Residues in contact with ARG 22 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12D SER 4.1 0.4 + - - -
13D HIS* 4.0 19.3 + - - +
14D VAL* 3.3 32.2 + - + +
15D VAL 3.6 13.7 + - - -
17D GLY 2.9 38.9 + - - +
18D TYR* 3.4 48.6 + - - -
19D VAL 3.1 14.5 + - - +
20D GLY 3.0 0.2 - - - -
21D ASN* 1.3 79.1 - - - +
23D ALA* 1.3 56.2 + - - +
25D THR* 4.6 2.7 + - - -
26D PHE* 4.6 8.5 + - - +
293D MET* 4.5 0.9 - - - +
25G THR* 4.7 12.2 - - - +
29G GLN* 5.0 2.2 + - - -
34G GLU* 4.7 0.2 + - - -
35G VAL* 3.1 30.1 + - - +
37G ALA* 3.8 18.4 - - - +
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Residues in contact with ALA 23 (chain D).
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 3.6 8.5 - - - +
19D VAL* 3.4 26.8 + - - +
20D GLY 3.0 6.6 + - - +
22D ARG* 1.3 79.2 - - - +
24D ALA* 1.3 58.3 + - - +
27D PRO* 3.1 24.7 - - - +
232D GLY 4.1 16.4 - - - +
235D ASP* 4.5 0.4 - - + -
236D LEU* 3.5 16.8 - - + +
291D LEU* 4.9 0.7 - - + -
293D MET* 3.6 16.9 - - + +
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Residues in contact with ALA 24 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9D SER* 4.6 3.6 - - - +
11D GLN* 3.4 29.6 - - - +
20D GLY 3.1 9.2 + - - +
21D ASN* 3.1 4.6 + - - +
23D ALA* 1.3 77.0 - - - +
25D THR* 1.3 64.0 + - - +
27D PRO* 3.2 12.1 - - - +
28D LEU* 3.4 23.1 + - + +
81D LEU* 4.6 2.2 - - + -
235D ASP 4.2 7.0 - - - +
239D ALA* 3.7 23.0 - - + +
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Residues in contact with THR 25 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9D SER* 6.5 0.2 - - - -
21D ASN* 2.5 43.0 + - - +
22D ARG* 5.2 1.1 - - - -
24D ALA* 1.3 71.1 - - - +
26D PHE* 1.3 66.8 + - - +
27D PRO 3.4 0.2 - - - -
28D LEU* 3.4 2.0 + - - +
29D GLN* 2.9 53.4 + - + +
35D VAL* 4.1 25.6 - - + +
37D ALA* 4.8 4.0 - - + +
22G ARG* 4.6 11.9 - - - +
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Residues in contact with PHE 26 (chain D).
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* 5.7 0.2 - - + -
22D ARG 4.6 9.1 + - - +
25D THR* 1.3 73.8 - - - +
27D PRO* 1.3 64.2 - - + +
29D GLN* 3.0 9.3 + - - +
30D VAL* 2.7 63.1 + - + +
293D MET* 3.6 31.4 - - + -
294D VAL* 4.4 13.7 - - + -
297D LYS* 3.9 37.9 - - + -
300D ILE* 4.5 7.2 - - + -
26G PHE* 4.2 8.5 - + - -
29G GLN* 3.3 43.5 - - + +
30G VAL* 4.0 15.0 - - + -
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Residues in contact with PRO 27 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23D ALA 3.1 25.6 - - - +
24D ALA* 3.2 13.7 - - - +
26D PHE* 1.3 95.6 - - + +
28D LEU* 1.3 62.7 + - - +
30D VAL* 3.4 1.5 + - + +
31D LEU* 2.9 32.2 + - + +
236D LEU* 3.2 24.7 - - + -
239D ALA* 4.6 5.2 - - + -
240D MET* 4.2 16.6 - - + +
293D MET* 4.2 7.4 - - - -
300D ILE* 4.2 17.3 - - + -
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Residues in contact with LEU 28 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7D VAL* 4.2 26.2 - - + -
9D SER* 5.3 2.5 - - - -
24D ALA 3.4 18.6 + - - +
25D THR 4.0 0.2 - - - +
27D PRO* 1.3 79.0 - - - +
29D GLN* 1.3 57.6 + - - +
31D LEU* 3.1 7.1 + - - +
32D GLY 3.0 8.8 + - - -
33D PHE* 3.0 33.7 + - + -
35D VAL* 3.8 25.6 - - + -
81D LEU* 4.2 17.0 - - + -
239D ALA* 2.9 32.8 - - + +
240D MET* 5.1 0.2 - - - -
242D LEU* 3.8 18.4 - - + -
243D ALA* 4.2 9.9 - - + -
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Residues in contact with GLN 29 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25D THR* 2.9 50.9 + - + +
26D PHE* 3.0 6.7 + - - +
28D LEU* 1.3 71.0 - - - +
30D VAL* 1.3 61.6 + - - +
31D LEU 2.6 10.5 + - - -
32D GLY 2.7 3.8 + - - -
33D PHE 4.0 5.4 - - - +
35D VAL* 4.0 10.9 - - + +
18G TYR* 3.1 36.6 + - - -
22G ARG* 4.7 5.3 + - - +
26G PHE* 3.5 35.1 - - + +
29G GLN* 5.4 0.9 - - - +
293G MET* 5.5 0.2 - - - +
294G VAL* 2.7 37.3 - - + +
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Residues in contact with VAL 30 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26D PHE* 2.7 61.0 + - + +
27D PRO* 3.5 9.9 - - + +
29D GLN* 1.3 71.0 - - - +
31D LEU* 1.3 61.8 + - + +
32D GLY 3.4 0.2 - - - -
297D LYS* 4.3 5.2 - - + +
300D ILE* 3.8 25.4 - - + -
301D GLU* 3.9 19.5 - - + +
26G PHE* 4.0 9.4 - - + -
297G LYS* 3.5 37.0 + - + +
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Residues in contact with LEU 31 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1D MET* 2.8 23.9 + - - +
27D PRO 2.9 26.9 + - - +
28D LEU* 3.2 9.6 - - - +
29D GLN 2.6 2.4 + - - -
30D VAL* 1.3 84.6 - - + +
32D GLY* 1.3 55.4 + - - -
33D PHE* 3.6 9.7 - - + -
240D MET* 4.6 14.6 - - + -
243D ALA* 3.5 25.8 - - + -
244D TRP* 4.2 22.9 - - + -
300D ILE* 4.0 26.9 - - + +
301D GLU* 4.2 15.0 - - - +
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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