Contacts of the helix formed by residues 17 - 31 (chain A) in PDB entry 5FOR
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 ALA 17 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13A TYR* 4.1 2.9 - - + -
14A SER 2.9 11.3 + - - +
16A ASP* 1.3 76.0 + - - +
18A GLU* 1.3 63.7 + - - +
19A GLU 3.3 3.6 - - - -
20A TRP* 3.1 18.3 + - + +
21A CYS* 3.1 9.4 + - - +
67A LEU* 3.8 24.3 - - + +
69A SER* 4.0 23.3 - - - +
100A CYS* 4.1 18.6 - - - -
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Residues in contact with GLU 18 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A TYR* 3.5 27.0 + - - -
14A SER 3.5 1.8 + - - -
15A PRO* 3.2 18.1 + - - +
16A ASP 3.5 0.8 - - - -
17A ALA* 1.3 76.9 - - - +
19A GLU* 1.3 63.5 + - + +
21A CYS* 3.2 7.1 + - - +
22A GLN* 3.1 48.1 + - - +
43A ARG* 2.1 38.0 + - - -
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Residues in contact with GLU 19 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A ALA 3.3 0.8 - - - -
18A GLU* 1.3 77.6 - - + +
20A TRP* 1.3 60.2 + - - +
21A CYS 3.1 1.3 - - - -
22A GLN* 3.2 19.1 + - + +
23A TYR* 2.9 30.5 + - - +
1140A 1PE 3.1 43.3 - - - +
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Residues in contact with TRP 20 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17A ALA* 3.1 15.2 + - + +
19A GLU* 1.3 78.5 - - - +
21A CYS* 1.3 62.0 + - - +
23A TYR* 3.5 32.1 + + - +
24A LEU* 3.1 32.9 + - + +
67A LEU* 3.7 14.4 - - + -
98A LEU* 3.6 21.8 - - + -
100A CYS* 3.4 25.5 - - - -
123A CYS* 3.5 45.7 - - + -
130A TYR* 3.7 27.1 - + - -
1140A 1PE 3.3 45.6 - - - -
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Residues in contact with CYS 21 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11A ILE* 4.0 12.4 - - - +
13A TYR* 3.6 50.5 - - + -
17A ALA 3.1 5.3 + - - +
18A GLU* 3.4 11.2 - - - +
19A GLU 3.1 0.6 - - - -
20A TRP* 1.3 76.6 - - - +
22A GLN* 1.3 65.7 + - - +
24A LEU* 3.4 2.7 + - - +
25A GLN* 3.2 26.3 + - - +
41A THR* 3.8 23.6 - - - -
67A LEU* 3.6 10.1 - - + +
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Residues in contact with GLN 22 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18A GLU* 3.1 36.0 + - - +
19A GLU* 3.2 22.3 + - + +
21A CYS* 1.3 77.1 - - - +
23A TYR* 1.3 63.3 + - - +
25A GLN* 3.3 16.2 + - - +
26A THR* 3.1 33.1 + - + +
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Residues in contact with TYR 23 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19A GLU 2.9 17.5 + - - +
20A TRP* 3.6 22.7 - + - +
22A GLN* 1.3 76.4 - - - +
24A LEU* 1.3 67.3 + - + +
26A THR* 3.0 14.3 + - - -
27A LEU* 3.0 36.9 + - + +
127A PRO* 3.8 28.8 - - - +
130A TYR* 4.0 24.0 - + - -
1140A 1PE 3.4 48.2 + - - -
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Residues in contact with LEU 24 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A ILE* 4.1 9.0 - - + -
20A TRP* 3.1 22.6 + - + +
21A CYS 4.1 2.7 - - - +
22A GLN 3.3 0.2 - - - -
23A TYR* 1.3 93.9 - - + +
25A GLN* 1.3 61.2 + - - +
27A LEU* 4.2 5.6 - - + -
28A PHE* 2.8 60.8 + - + -
65A VAL* 4.5 12.8 - - + -
67A LEU* 3.7 30.5 - - + -
98A LEU* 4.6 9.6 - - + -
121A LEU* 6.2 1.1 - - + -
130A TYR* 4.3 22.9 - - + -
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Residues in contact with GLN 25 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11A ILE* 4.3 8.9 - - + +
21A CYS* 3.2 25.4 + - - +
22A GLN* 3.5 19.9 + - - +
24A LEU* 1.3 78.0 - - - +
26A THR* 1.3 64.7 + - + +
28A PHE* 3.7 3.3 - - - +
29A LEU* 3.0 38.2 + - + +
39A ILE* 5.0 13.8 + - + +
41A THR* 3.7 29.9 + - + +
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Residues in contact with THR 26 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22A GLN* 3.1 21.4 + - + +
23A TYR* 3.0 16.0 + - - -
25A GLN* 1.3 76.4 - - + +
27A LEU* 1.3 65.2 + - - +
29A LEU* 3.6 7.9 + - - +
30A SER* 2.8 30.5 + - - -
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Residues in contact with LEU 27 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A TYR* 3.0 32.5 + - + +
24A LEU* 3.7 5.8 - - + +
25A GLN 3.2 0.4 - - - -
26A THR* 1.3 84.4 + - - +
28A PHE* 1.3 68.5 + - + +
30A SER* 3.1 14.9 + - - -
31A SER* 3.2 12.5 + - - -
127A PRO* 4.0 14.1 - - + +
130A TYR* 3.9 37.2 - - + -
131A VAL* 3.9 13.7 - - + -
1141A I3C 3.4 39.5 - - + +
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Residues in contact with PHE 28 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9A ILE* 4.4 11.7 - - + -
11A ILE* 4.2 18.4 - - + -
24A LEU* 2.8 51.7 + - + +
25A GLN* 3.7 3.6 - - - +
27A LEU* 1.3 85.1 - - + +
29A LEU* 1.3 59.0 + - - +
30A SER 3.5 0.3 + - - -
31A SER* 3.6 3.0 + - - -
34A VAL* 3.1 35.3 - - + +
35A ARG* 3.2 13.2 + - - -
39A ILE* 3.7 26.7 - - + -
65A VAL* 4.7 5.4 - - + -
121A LEU* 6.5 0.2 - - + -
130A TYR* 4.2 8.5 - - + -
131A VAL* 4.2 17.0 - - + -
134A VAL* 3.4 37.2 - - + -
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Residues in contact with LEU 29 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25A GLN* 3.0 28.3 + - + +
26A THR* 3.9 7.2 - - - +
28A PHE* 1.3 75.2 - - - +
30A SER* 1.3 58.0 + - - +
31A SER 3.4 0.4 - - - -
35A ARG* 2.5 58.9 + - + +
37A GLN 5.1 2.2 - - - +
39A ILE* 3.8 26.7 - - + -
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Residues in contact with SER 30 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A THR* 2.8 21.0 + - - -
27A LEU* 3.1 8.8 + - - -
29A LEU* 1.3 80.7 - - - +
31A SER* 1.3 60.2 + - - +
32A ARG 3.9 0.7 + - - -
35A ARG* 4.6 6.3 - - - +
1141A I3C 3.2 35.2 + - - +
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Residues in contact with SER 31 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27A LEU 3.2 14.1 + - - -
28A PHE 3.6 4.4 + - - -
29A LEU 3.4 0.8 - - - -
30A SER* 1.3 78.4 - - - +
32A ARG* 1.3 58.9 + - - +
33A GLN* 3.1 19.8 + - - +
34A VAL* 4.3 4.4 - - - +
35A ARG* 2.7 38.4 + - - +
131A VAL* 3.9 16.0 - - - +
1141A I3C 3.3 32.4 + - - -
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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