Contacts of the helix formed by residues 20 - 33 (chain A) in PDB entry 2FY4
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 PRO 20 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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18A VAL 3.7 1.9 - - - +
19A PRO* 1.3 91.1 - - + +
21A LEU* 1.3 67.6 + - - +
22A GLN* 3.5 2.2 - - + +
23A GLN* 3.3 40.1 + - + +
24A THR* 3.3 18.0 + - - -
62A GLN* 4.1 4.5 - - - +
500A MET* 4.1 8.7 - - + -
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Residues in contact with LEU 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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19A PRO 3.5 2.2 + - - -
20A PRO* 1.3 71.1 - - - +
22A GLN* 1.3 79.8 + - + +
24A THR* 3.1 5.0 + - - -
25A LEU* 3.0 46.6 + - + +
51A PHE* 4.4 4.3 - - + -
52A GLY* 4.4 6.5 - - - -
58A GLY* 3.4 34.5 - - - +
59A GLU* 3.6 15.3 - - + +
62A GLN* 3.7 21.6 - - + +
505A HIS* 4.0 8.1 - - + -
509A LEU* 3.9 28.9 - - + -
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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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20A PRO* 3.5 2.6 - - + +
21A LEU* 1.3 91.5 - - + +
23A GLN* 1.3 57.9 + - - +
25A LEU* 3.9 13.4 - - - +
26A ALA* 3.0 31.2 + - - +
52A GLY* 3.0 29.6 + - - +
59A GLU* 4.7 7.9 + - - -
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Residues in contact with GLN 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 PRO* 4.1 3.4 - - - +
20A PRO* 3.3 37.9 + - + +
21A LEU 3.2 0.8 - - - -
22A GLN* 1.3 79.5 - - - +
24A THR* 1.3 57.4 + - - +
26A ALA* 3.8 4.0 - - - +
27A THR* 3.0 39.8 + - - +
495A MET* 5.1 5.4 - - - -
500A MET* 3.3 55.5 + - - +
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Residues in contact with THR 24 (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 PRO* 3.6 12.5 - - - +
20A PRO 3.3 1.8 + - - -
21A LEU* 3.1 7.9 + - + -
23A GLN* 1.3 79.5 - - - +
25A LEU* 1.3 60.1 + - + +
27A THR* 3.8 1.3 - - - -
28A TYR* 2.9 28.1 + - - +
500A MET 5.1 0.6 + - - -
501A ALA 3.9 6.2 + - - -
502A ILE* 3.8 28.9 - - + +
505A HIS* 2.6 37.7 + - + +
506A LEU* 3.9 26.9 - - + -
509A LEU* 5.7 1.3 - - + -
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Residues in contact with LEU 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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21A LEU* 3.0 37.0 + - + +
22A GLN* 3.9 15.5 - - - +
24A THR* 1.3 79.1 - - + +
26A ALA* 1.3 63.7 + - - +
28A TYR* 3.3 5.4 + - + +
29A LEU* 3.1 28.7 + - - +
48A VAL* 3.8 23.7 - - + +
51A PHE* 4.1 15.0 - - + -
52A GLY* 3.7 31.4 - - - +
506A LEU* 4.7 8.5 - - + -
523A MET* 4.1 25.8 - - + -
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Residues in contact with ALA 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 3.0 18.8 + - - +
23A GLN* 3.8 4.9 - - - +
25A LEU* 1.3 78.7 - - - +
27A THR* 1.3 64.0 + - - +
29A LEU* 3.4 8.3 + - - +
30A GLN* 3.1 24.1 + - - +
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Residues in contact with THR 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 GLN* 3.0 24.5 + - - +
26A ALA* 1.3 76.3 - - - +
28A TYR* 1.3 57.9 + - - +
30A GLN* 3.2 6.6 + - + +
31A CYS* 2.8 49.5 + - - -
492A TYR* 4.3 1.8 - - + -
495A MET* 3.9 29.3 - - + -
502A ILE* 3.5 26.2 - - + -
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Residues in contact with TYR 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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24A THR 2.9 19.4 + - - +
25A LEU* 3.4 6.7 - - - +
26A ALA 3.3 0.2 - - - -
27A THR* 1.3 76.2 - - - +
29A LEU* 1.3 71.3 + - + +
31A CYS* 3.0 13.8 + - + +
32A MET* 3.1 28.9 + - + +
44A SER* 5.8 0.7 - - - -
48A VAL* 4.1 19.3 - - + -
453A ARG* 6.2 1.3 - - - -
502A ILE* 3.8 19.5 - - + +
506A LEU* 4.1 17.0 - - + -
523A MET* 3.5 32.9 + - + -
526A ASP* 4.5 4.8 + - - -
528A THR* 3.5 13.1 - - + +
529A TYR* 3.0 44.0 + + + +
532A SER* 4.2 15.9 - - - -
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Residues in contact with LEU 29 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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25A LEU 3.1 14.4 + - - +
26A ALA* 3.8 8.3 - - - +
28A TYR* 1.3 84.7 - - + +
30A GLN* 1.3 58.1 + - - +
32A MET* 3.1 4.5 + - + -
33A ARG* 2.9 26.7 + - - +
41A PHE* 3.5 31.7 - - + -
44A SER* 4.1 8.3 - - - +
45A GLN* 4.1 27.4 - - + +
48A VAL* 3.6 43.3 - - + -
528A THR* 6.2 1.6 - - + -
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Residues in contact with GLN 30 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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26A ALA 3.1 18.1 + - - +
27A THR* 3.6 7.4 - - - +
29A LEU* 1.3 76.5 - - - +
31A CYS* 1.3 63.5 + - - +
32A MET 3.4 0.5 + - - -
33A ARG* 3.8 23.9 + - - +
34A HIS* 3.9 9.0 + - - -
41A PHE* 5.8 0.2 - - - -
457A PRO* 3.1 36.4 - - + +
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Residues in contact with CYS 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 THR* 2.8 43.2 + - - -
28A TYR* 3.0 9.6 + - + +
30A GLN* 1.3 76.1 - - - +
32A MET* 1.3 63.8 + - + +
34A HIS* 3.2 21.6 - - - -
35A LEU* 3.7 12.8 - - - +
453A ARG* 4.2 18.8 - - + -
455A ALA 4.3 1.9 - - - +
456A THR* 6.3 0.9 - - - +
457A PRO* 5.7 2.2 - - - -
492A TYR* 3.8 24.2 - - - -
502A ILE* 4.2 6.5 - - + -
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Residues in contact with MET 32 (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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28A TYR* 3.1 27.1 + - + +
29A LEU* 3.1 5.8 + - - +
31A CYS* 1.3 85.9 - - + +
33A ARG* 1.3 66.3 + - - +
34A HIS 3.3 3.1 - - - -
35A LEU* 2.9 28.6 + - + +
36A VAL* 3.3 21.4 + - + +
41A PHE* 4.8 2.0 - - + -
434A PRO* 4.9 0.9 - - - -
453A ARG* 4.5 8.5 - - - -
528A THR* 3.8 24.2 - - + +
531A MET* 3.1 35.9 - - + -
532A SER* 3.4 35.9 - - - -
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Residues in contact with ARG 33 (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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29A LEU 2.9 10.7 + - - +
30A GLN* 3.8 23.2 + - - +
31A CYS 3.7 0.8 - - - -
32A MET* 1.3 77.9 - - - +
34A HIS* 1.3 63.7 + - - +
35A LEU 3.3 0.3 + - - -
36A VAL* 3.3 18.9 + - - +
41A PHE* 3.4 59.5 - - + +
45A GLN* 4.5 7.3 - - - +
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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