Contacts of the helix formed by residues 20 - 32 (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 GLY 20 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11G GLN* 3.8 18.2 - - - +
12G SER* 3.0 25.1 + - - -
19G VAL* 1.3 75.3 - - - +
21G ASN* 1.3 65.6 + - - -
23G ALA* 2.9 13.2 + - - +
24G ALA* 3.1 10.6 + - - +
84G TYR* 5.5 0.2 - - - -
235G ASP* 3.7 18.0 + - - +
6401G PLP 3.9 0.8 - - - -
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Residues in contact with ASN 21 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9G SER* 2.6 42.0 + - - +
11G GLN* 2.9 38.9 + - - +
12G SER 2.6 12.0 + - - +
13G HIS* 5.2 1.8 - - + +
20G GLY* 1.3 71.2 - - - -
22G ARG* 1.3 55.6 + - - +
24G ALA* 3.6 4.4 - - - +
25G THR* 2.7 49.5 + - - +
37G ALA* 4.4 8.5 - - + +
38G VAL 3.0 10.2 - - - +
39G ASN* 3.3 19.1 - - - +
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Residues in contact with ARG 22 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25D THR* 4.6 11.3 - - - +
29D GLN* 4.7 5.4 + - - +
35D VAL 2.8 30.3 + - - -
37D ALA* 3.6 25.7 - - - +
12G SER 4.2 0.8 + - - -
13G HIS* 4.0 18.2 - - - +
14G VAL* 3.4 30.5 - - + +
15G VAL 3.6 9.3 + - - -
17G GLY 3.1 31.8 + - - +
18G TYR* 3.4 48.6 + - - -
19G VAL 3.1 13.7 + - - +
20G GLY 3.0 0.4 + - - -
21G ASN* 1.3 79.3 - - - +
23G ALA* 1.3 57.3 + - - +
25G THR* 4.5 2.8 + - - -
26G PHE* 4.6 8.3 + - - +
293G MET* 4.6 0.9 - - - +
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Residues in contact with ALA 23 (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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18G TYR* 3.6 8.1 - - + +
19G VAL* 3.4 23.3 + - - +
20G GLY 2.9 8.0 + - - +
22G ARG* 1.3 78.8 - - - +
24G ALA* 1.3 58.0 + - - +
25G THR 3.7 0.2 - - - -
27G PRO* 3.0 26.3 - - - +
232G GLY 4.1 16.6 - - - +
235G ASP* 4.4 4.3 - - + -
236G LEU* 3.5 14.1 - - + +
291G LEU* 4.9 0.7 - - + -
293G MET* 3.7 17.4 - - + +
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Residues in contact with ALA 24 (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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9G SER* 4.5 2.7 - - - +
11G GLN* 3.3 31.0 - - - +
20G GLY 3.1 8.0 + - - +
21G ASN* 3.1 4.1 + - - +
23G ALA* 1.3 79.1 - - - +
25G THR* 1.3 64.5 + - - +
26G PHE 3.5 0.4 - - - -
27G PRO* 3.4 6.6 - - - +
28G LEU* 3.4 23.8 + - + +
81G LEU* 4.4 4.0 - - + -
235G ASP 4.3 6.7 - - - +
239G ALA* 3.7 24.0 - - + +
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Residues in contact with THR 25 (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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22D ARG* 4.7 9.9 - - - +
9G SER* 6.5 0.4 - - - -
21G ASN* 2.7 40.6 + - - +
22G ARG* 5.3 1.1 - - - -
24G ALA* 1.3 71.8 - - - +
26G PHE* 1.3 65.5 + - - +
28G LEU* 3.5 1.7 + - - +
29G GLN* 2.7 57.0 + - + +
35G VAL* 4.0 25.3 - - + +
37G ALA* 4.7 5.7 - - + +
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Residues in contact with PHE 26 (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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26D PHE* 4.2 7.4 - + - -
29D GLN* 3.5 45.5 - - + +
30D VAL* 4.0 15.0 - - + -
22G ARG 4.6 8.9 + - - +
25G THR* 1.3 74.8 - - - +
27G PRO* 1.3 66.0 - - + +
29G GLN* 2.9 8.3 + - - +
30G VAL* 2.7 64.5 + - + +
293G MET* 3.5 32.3 - - + -
294G VAL* 4.4 11.4 - - - -
297G LYS* 3.7 37.9 - - + -
300G ILE* 4.5 5.2 - - + -
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Residues in contact with PRO 27 (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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23G ALA 3.0 27.8 - - - +
24G ALA* 3.4 7.4 - - - +
26G PHE* 1.3 93.9 - - + +
28G LEU* 1.3 65.0 + - - +
30G VAL* 3.3 9.3 + - + +
31G LEU* 2.8 30.0 + - + +
236G LEU* 3.2 24.2 - - + -
239G ALA* 4.7 4.7 - - + -
240G MET* 4.1 17.5 - - + -
293G MET* 4.0 10.5 - - - -
300G ILE* 4.1 10.3 - - + -
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Residues in contact with LEU 28 (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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7G VAL* 4.2 20.4 - - + -
9G SER* 5.3 2.0 - - - -
24G ALA* 3.4 18.8 + - + +
25G THR* 5.3 0.2 - - - -
26G PHE 3.4 0.4 - - - -
27G PRO* 1.3 77.9 - - - +
29G GLN* 1.3 58.9 + - - +
31G LEU* 3.1 6.7 + - + +
32G GLY 3.0 9.2 + - - -
33G PHE* 2.9 33.6 + - + +
35G VAL* 3.8 26.5 - - + -
81G LEU* 4.2 21.8 - - + -
239G ALA* 2.9 33.4 - - + +
240G MET* 5.0 0.2 - - - -
242G LEU* 4.0 16.8 - - + -
243G ALA* 4.2 10.3 - - + -
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Residues in contact with GLN 29 (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* 3.2 38.0 + - - -
22D ARG* 4.9 3.0 - - - +
26D PHE* 3.3 34.8 - - + +
29D GLN* 5.4 0.9 - - - +
294D VAL* 2.8 26.6 - - + +
25G THR* 2.7 49.3 + - + +
26G PHE* 2.9 7.2 + - - +
28G LEU* 1.3 72.9 - - - +
30G VAL* 1.3 64.4 + - - +
31G LEU 2.7 6.2 + - - -
32G GLY 2.7 11.8 + - - -
33G PHE 3.9 9.9 - - - +
35G VAL* 4.0 11.2 - - + +
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Residues in contact with VAL 30 (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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26D PHE* 4.0 10.1 - - + -
294D VAL* 4.9 0.2 - - - -
297D LYS* 3.6 27.9 + - + -
26G PHE* 2.7 61.5 + - + +
27G PRO* 3.4 10.1 - - + +
29G GLN* 1.3 71.8 - - - +
31G LEU* 1.3 62.2 + - + +
32G GLY 3.7 0.2 + - - -
297G LYS* 4.3 5.4 - - + +
300G ILE* 3.7 26.2 - - + -
301G GLU* 4.1 26.4 - - + +
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Residues in contact with LEU 31 (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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1G MET* 3.1 27.5 + - - +
27G PRO 2.8 26.1 + - - +
28G LEU* 3.3 9.2 - - - +
29G GLN 2.7 1.6 + - - -
30G VAL* 1.3 80.7 - - - +
32G GLY* 1.3 54.6 + - - -
33G PHE* 3.7 10.6 - - + -
240G MET* 4.6 15.0 - - + -
243G ALA* 3.5 26.2 - - + -
244G TRP* 4.1 23.3 - - + -
300G ILE* 4.0 28.9 - - + +
301G GLU* 4.2 14.4 - - - +
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Residues in contact with GLY 32 (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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294D VAL* 4.2 11.0 - - - +
295D GLN* 5.4 4.9 + - - -
1G MET* 3.2 31.2 - - - +
3G GLU 4.9 0.2 - - - +
29G GLN 2.7 18.1 + - - -
30G VAL 3.4 0.8 + - - -
31G LEU* 1.3 73.3 - - - +
33G PHE* 1.3 64.8 + - - +
34G GLU* 3.7 0.9 + - - +
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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