Contacts of the helix formed by residues 20 - 31 (chain H) 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 H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11H GLN* 3.6 19.3 - - - +
12H SER* 3.1 23.3 + - - -
19H VAL* 1.3 73.4 - - - +
21H ASN* 1.3 65.7 + - - -
23H ALA* 2.9 12.5 + - - +
24H ALA* 3.1 12.0 + - - +
84H TYR* 5.5 0.2 - - - -
235H ASP* 3.9 18.5 + - - +
7401H PLP 4.0 1.0 - - - -
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Residues in contact with ASN 21 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9H SER* 2.7 40.2 + - - +
11H GLN* 3.1 19.0 + - - +
12H SER 2.6 12.7 + - - +
13H HIS* 5.1 2.2 - - + +
20H GLY* 1.3 71.5 - - - -
22H ARG* 1.3 55.9 + - - +
24H ALA* 3.6 4.9 - - - +
25H THR* 2.6 48.4 + - - +
37H ALA* 4.2 10.0 - - + +
38H VAL 2.9 27.5 - - - +
39H ASN* 3.2 19.2 - - - +
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Residues in contact with ARG 22 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25C THR* 4.8 6.2 - - - +
29C GLN* 5.1 5.0 + - - +
35C VAL* 2.2 41.1 + - - +
36C ASP* 4.3 0.2 + - - -
37C ALA* 3.1 30.4 - - - +
12H SER 4.2 0.4 + - - -
13H HIS* 3.9 18.4 - - - +
14H VAL* 3.3 32.5 + - + +
15H VAL 3.9 5.2 - - - -
17H GLY 3.0 33.9 + - - +
18H TYR* 3.4 43.7 + - - -
19H VAL 3.2 13.0 + - - +
20H GLY 3.0 0.6 - - - -
21H ASN* 1.3 79.3 - - - +
23H ALA* 1.3 57.3 + - - +
25H THR* 4.5 3.1 + - - -
26H PHE* 4.6 8.5 + - - +
293H MET* 4.4 0.9 - - - +
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Residues in contact with ALA 23 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18H TYR* 3.6 8.5 - - + +
19H VAL* 3.5 23.1 + - - +
20H GLY 2.9 8.0 + - - +
22H ARG* 1.3 79.3 - - - +
24H ALA* 1.3 58.6 + - - +
27H PRO* 3.0 25.9 - - - +
232H GLY 4.1 15.7 - - - +
235H ASP* 4.5 0.4 - - + -
236H LEU* 3.5 18.6 - - + +
291H LEU* 4.9 0.9 - - + -
293H MET* 3.6 17.1 - - + +
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Residues in contact with ALA 24 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9H SER* 4.5 4.3 - - - +
11H GLN* 3.4 30.1 - - - +
20H GLY 3.1 10.2 + - - +
21H ASN* 4.0 3.1 - - - +
23H ALA* 1.3 77.8 - - - +
25H THR* 1.3 64.7 + - - +
27H PRO* 3.3 8.8 - - - +
28H LEU* 3.4 23.9 + - + +
81H LEU* 4.6 3.4 - - + -
235H ASP 4.4 6.7 - - - +
239H ALA* 3.7 21.6 - - + +
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Residues in contact with THR 25 (chain H).
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* 4.9 8.3 - - - +
9H SER* 6.5 0.2 - - - -
21H ASN* 2.6 41.4 + - - +
22H ARG 5.3 0.4 - - - -
24H ALA* 1.3 71.1 - - - +
26H PHE* 1.3 67.3 + - - +
28H LEU* 3.5 4.4 + - - +
29H GLN* 2.9 54.1 + - + +
35H VAL* 3.9 24.8 - - + +
37H ALA* 4.7 4.5 - - + +
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Residues in contact with PHE 26 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26C PHE* 4.7 5.2 - + - -
29C GLN* 2.9 60.3 + - + +
30C VAL* 3.8 9.9 - - + -
22H ARG 4.6 7.0 + - - +
25H THR* 1.3 74.9 - - - +
27H PRO* 1.3 66.8 - - + +
29H GLN* 2.8 9.8 + - - +
30H VAL* 2.7 60.7 + - + +
293H MET* 3.5 33.9 - - + -
294H VAL* 4.3 9.4 - - - -
297H LYS* 3.8 37.2 - - + -
300H ILE* 4.5 5.2 - - + -
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Residues in contact with PRO 27 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23H ALA 3.0 27.8 - - - +
24H ALA* 3.3 10.3 - - - +
26H PHE* 1.3 94.9 - - + +
28H LEU* 1.3 63.1 + - - +
30H VAL* 3.4 2.8 + - + +
31H LEU* 2.9 32.0 + - - +
236H LEU* 3.2 24.9 - - + -
239H ALA* 4.6 4.3 - - + -
240H MET* 4.0 19.1 - - + +
293H MET* 4.1 8.5 - - - -
300H ILE* 4.1 17.5 - - + -
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Residues in contact with LEU 28 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7H VAL* 4.4 17.3 - - + -
9H SER* 5.3 2.0 - - - -
24H ALA* 3.4 21.2 + - + +
26H PHE 3.4 0.6 - - - -
27H PRO* 1.3 78.9 - - - +
29H GLN* 1.3 57.5 + - - +
31H LEU* 3.3 6.0 + - - +
32H GLY 3.1 8.0 + - - -
33H PHE* 2.9 34.8 + - + +
35H VAL* 3.8 28.3 - - + -
81H LEU* 4.1 22.0 - - + -
239H ALA* 2.9 32.5 - - + +
240H MET* 4.9 0.2 - - - -
242H LEU* 4.1 17.3 - - + -
243H ALA* 4.3 10.1 - - + -
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Residues in contact with GLN 29 (chain H).
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* 3.8 30.9 + - - -
22C ARG* 5.2 6.1 + - - +
26C PHE* 3.1 43.7 - - + +
29C GLN* 4.5 4.2 - - - +
294C VAL* 3.3 19.6 - - + +
297C LYS* 5.1 1.0 - - - +
25H THR* 2.9 48.1 + - + +
26H PHE* 2.8 7.8 + - - +
28H LEU* 1.3 72.8 - - - +
30H VAL* 1.3 58.7 + - - +
31H LEU 2.7 4.5 - - - -
32H GLY* 2.7 19.1 + - - -
33H PHE 4.0 9.2 - - - +
35H VAL* 4.1 12.5 - - + +
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Residues in contact with VAL 30 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26C PHE* 4.2 8.7 - - + -
30C VAL* 4.8 2.0 - - + -
297C LYS* 3.2 32.3 + - + -
26H PHE* 2.7 57.3 + - + +
27H PRO* 3.5 10.1 - - + +
29H GLN* 1.3 71.0 - - - +
31H LEU* 1.3 61.3 + - + +
32H GLY 3.4 0.2 - - - -
297H LYS* 4.2 8.5 - - + +
300H ILE* 3.9 20.2 - - + -
301H GLU* 3.9 32.3 - - + +
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Residues in contact with LEU 31 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1H MET* 2.9 28.0 + - - +
27H PRO 2.9 26.2 + - - +
28H LEU* 3.3 9.2 - - - +
29H GLN 2.7 0.2 - - - -
30H VAL* 1.3 80.6 - - - +
32H GLY* 1.3 55.9 + - - +
33H PHE* 3.7 10.3 - - + -
240H MET* 4.6 14.4 - - + -
243H ALA* 3.5 25.8 - - + -
244H TRP* 4.2 25.1 - - + -
300H ILE* 4.1 30.5 - - + +
301H GLU* 4.3 11.4 - - - +
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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