Contacts of the helix formed by residues 20 - 32 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11C GLN* 3.7 17.6 - - - +
12C SER* 3.1 24.7 + - - -
19C VAL* 1.3 76.2 - - - +
21C ASN* 1.3 64.3 + - - -
23C ALA* 2.9 12.6 + - - +
24C ALA* 3.1 11.1 + - - +
84C TYR* 5.4 0.2 - - - -
235C ASP* 3.8 18.9 + - - +
2401C PLP 3.9 1.0 - - - -
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Residues in contact with ASN 21 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9C SER* 2.7 39.4 + - - +
11C GLN* 3.0 20.4 + - - +
12C SER 2.6 11.8 + - - +
13C HIS* 5.1 2.5 - - + +
20C GLY* 1.3 71.4 - - - -
22C ARG* 1.3 55.8 + - - +
24C ALA* 4.2 4.1 - - - +
25C THR* 2.7 48.5 + - - +
37C ALA* 4.3 9.8 - - + +
38C VAL 2.9 27.4 - - - +
39C ASN* 3.1 19.7 - - - +
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Residues in contact with ARG 22 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12C SER 4.2 0.6 + - - -
13C HIS* 3.9 17.7 - - - +
14C VAL* 3.4 32.0 + - + +
15C VAL 3.7 6.8 + - - -
17C GLY 2.9 37.0 + - - +
18C TYR* 3.5 43.8 - - - -
19C VAL 3.1 13.7 + - - +
20C GLY 3.0 0.2 - - - -
21C ASN* 1.3 79.3 - - - +
23C ALA* 1.3 56.4 + - - +
25C THR* 4.5 2.9 + - - -
26C PHE* 4.6 9.0 + - - +
293C MET* 4.5 1.0 - - - +
25H THR* 4.9 7.3 - - - +
29H GLN* 5.2 5.0 + - - +
34H GLU* 4.5 0.2 + - - -
35H VAL* 2.6 36.3 + - - +
36H ASP* 4.5 0.4 + - - -
37H ALA* 3.4 27.3 - - - +
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Residues in contact with ALA 23 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18C TYR* 3.6 8.1 - - + +
19C VAL* 3.4 24.4 + - - +
20C GLY 2.9 8.2 + - - +
22C ARG* 1.3 79.5 - - - +
24C ALA* 1.3 58.5 + - - +
25C THR 3.8 0.2 - - - -
27C PRO* 3.2 24.0 - - - +
232C GLY 4.1 15.5 - - - +
235C ASP* 4.5 0.4 - - + -
236C LEU* 3.5 18.6 - - + +
291C LEU* 4.9 1.1 - - + -
293C MET* 3.7 16.1 - - + +
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Residues in contact with ALA 24 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9C SER* 4.5 3.1 - - - +
11C GLN* 3.3 30.3 - - - +
20C GLY 3.1 7.8 + - - +
21C ASN* 3.1 4.3 + - - +
23C ALA* 1.3 77.6 - - - +
25C THR* 1.3 64.4 + - - +
27C PRO* 3.2 9.7 - - - +
28C LEU* 3.5 22.8 + - + +
81C LEU* 4.4 4.0 - - + -
235C ASP 4.3 7.4 - - - +
239C ALA* 3.8 22.4 - - + +
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Residues in contact with THR 25 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9C SER* 6.5 0.4 - - - -
21C ASN* 2.7 37.1 + - - +
22C ARG* 5.3 1.1 - - - -
24C ALA* 1.3 71.2 - - - +
26C PHE* 1.3 65.2 + - - +
28C LEU* 4.0 0.7 - - - +
29C GLN* 2.8 56.7 + - + +
35C VAL* 4.0 26.3 - - + +
37C ALA* 4.7 4.7 - - + +
22H ARG* 4.8 9.2 - - - +
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Residues in contact with PHE 26 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22C ARG 4.6 7.5 + - - +
25C THR* 1.3 75.1 - - - +
27C PRO* 1.3 63.8 - - + +
29C GLN* 3.0 7.7 + - - -
30C VAL* 2.7 63.9 + - + +
293C MET* 3.5 34.1 - - + -
294C VAL* 4.3 10.8 - - - -
297C LYS* 3.8 37.0 - - + -
300C ILE* 4.5 5.6 - - + -
26H PHE* 4.7 4.7 - + - -
29H GLN* 3.1 58.3 + - + +
30H VAL* 3.9 10.1 - - + -
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Residues in contact with PRO 27 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23C ALA 3.2 28.5 - - - +
24C ALA 3.2 8.3 - - - +
26C PHE* 1.3 94.1 - - + +
28C LEU* 1.3 64.5 + - - +
30C VAL* 3.2 9.9 + - + +
31C LEU* 2.8 31.0 + - - +
236C LEU* 3.3 24.7 - - + -
239C ALA* 4.7 4.5 - - + -
240C MET* 4.2 16.6 - - + +
293C MET* 4.2 3.8 - - - -
300C ILE* 4.1 17.3 - - + -
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Residues in contact with LEU 28 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7C VAL* 4.1 27.4 - - + -
9C SER* 5.3 2.2 - - - -
24C ALA* 3.5 19.1 + - + +
26C PHE 3.4 0.4 - - - -
27C PRO* 1.3 78.2 - - - +
29C GLN* 1.3 59.0 + - - +
31C LEU* 3.1 7.7 + - + +
32C GLY 3.0 22.2 + - - -
33C PHE* 3.0 20.1 + - + -
35C VAL* 3.8 24.0 - - + -
81C LEU* 4.2 17.9 - - + -
239C ALA* 3.1 31.6 - - + +
240C MET* 5.0 0.4 - - - -
242C LEU* 3.9 16.4 - - + -
243C ALA* 4.2 10.3 - - + -
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Residues in contact with GLN 29 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25C THR* 2.8 50.3 + - + +
26C PHE* 3.3 5.5 + - - +
28C LEU* 1.3 72.5 - - - +
30C VAL* 1.3 64.2 + - - +
31C LEU 2.7 5.8 + - - -
32C GLY 2.8 11.8 + - - -
33C PHE 3.9 9.9 - - - +
35C VAL* 4.0 10.9 - - + +
18H TYR* 3.6 33.4 + - - +
22H ARG* 5.1 4.8 + - - +
26H PHE* 2.9 45.1 + - + +
29H GLN* 4.5 3.6 - - - +
293H MET* 5.1 0.2 - - - +
294H VAL* 3.0 18.4 - - + +
297H LYS* 4.9 1.2 - - - +
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Residues in contact with VAL 30 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26C PHE* 2.7 61.8 + - + +
27C PRO* 3.3 10.3 - - + +
29C GLN* 1.3 71.8 - - - +
31C LEU* 1.3 61.8 + - + +
32C GLY 3.4 0.4 + - - -
297C LYS* 4.4 6.5 - - + +
300C ILE* 3.8 25.4 - - + -
301C GLU* 4.0 26.5 - - + +
26H PHE* 3.8 7.4 - - + -
30H VAL* 4.8 2.5 - - + -
297H LYS* 3.1 33.9 + - + -
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Residues in contact with LEU 31 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1C MET* 3.5 26.6 + - - +
27C PRO 2.8 26.2 + - - +
28C LEU* 3.3 9.2 - - - +
29C GLN 2.7 1.4 - - - -
30C VAL* 1.3 85.4 - - + +
32C GLY* 1.3 56.1 + - - +
33C PHE* 3.7 10.1 - - + -
240C MET* 4.6 13.9 - - + -
243C ALA* 3.5 26.9 - - + -
244C TRP* 4.1 24.5 - - + -
300C ILE* 4.0 26.0 - - + +
301C GLU* 4.2 13.5 - - - +
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Residues in contact with GLY 32 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1C MET* 3.0 31.3 - - - +
3C GLU 4.4 1.6 - - - +
29C GLN 2.8 7.3 + - - -
30C VAL 3.4 0.6 - - - -
31C LEU* 1.3 80.6 - - - +
33C PHE* 1.3 63.7 + - - +
34C GLU 3.8 0.5 + - - -
294H VAL* 3.5 18.8 - - - +
295H GLN* 5.3 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