Contacts of the helix formed by residues 15 - 26 (chain H) in PDB entry 2FYU
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 ASP 15 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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165D TYR* 5.2 12.0 - - + -
167D GLU* 5.2 6.1 - - - +
178D THR* 3.5 23.3 - - + +
179D MET* 4.1 15.9 - - - +
180D SER* 3.4 27.7 + - - -
16H PRO* 1.4 74.3 - - - +
17H LEU* 4.0 13.6 + - - +
18H THR* 3.0 46.8 + - - +
19H THR* 4.1 2.7 + - - -
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Residues in contact with PRO 16 (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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178D THR* 3.7 19.7 - - + +
180D SER* 4.3 2.2 - - - -
15H ASP* 1.4 88.8 - - - +
17H LEU* 1.3 56.3 + - - +
18H THR 3.3 0.4 - - - -
19H THR* 3.4 16.0 - - - +
20H VAL* 3.1 33.6 + - + +
73H LEU* 4.6 2.5 - - - +
76H SER* 3.9 25.1 - - - +
77H LEU* 3.8 24.5 - - + -
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Residues in contact with LEU 17 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128D PHE* 5.9 0.4 - - + -
132D THR* 3.8 41.1 - - + +
179D MET* 4.3 14.8 - - + -
180D SER* 3.3 18.4 + - - +
15H ASP* 4.0 14.1 - - - +
16H PRO* 1.3 78.8 - - - +
18H THR* 1.3 56.7 + - - +
20H VAL* 3.9 0.5 - - - +
21H ARG* 3.0 69.7 + - + +
66H ASP* 5.7 1.3 - - - +
69H VAL* 4.3 11.2 - - + -
73H LEU* 3.8 25.9 - - + +
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Residues in contact with THR 18 (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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15H ASP* 3.0 26.2 + - - +
17H LEU* 1.3 73.6 - - - +
19H THR* 1.4 64.1 + - - +
21H ARG* 4.1 5.6 - - - +
22H GLU* 3.2 44.5 + - + +
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Residues in contact with THR 19 (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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15H ASP 4.3 1.9 + - - -
16H PRO* 3.4 23.9 + - - +
18H THR* 1.4 75.3 - - - +
20H VAL* 1.3 60.2 + - + +
22H GLU* 3.7 9.5 + - - +
23H GLN* 3.2 42.5 + - + +
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Residues in contact with VAL 20 (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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16H PRO* 3.1 20.4 + - + +
17H LEU 3.5 0.9 + - - +
18H THR 3.3 0.4 - - - -
19H THR* 1.3 77.0 - - + +
21H ARG* 1.3 54.4 + - - +
23H GLN* 3.3 11.9 + - - +
24H CYS* 2.9 37.3 + - - -
69H VAL* 3.8 35.2 - - + +
72H LYS* 4.6 13.5 - - + -
73H LEU* 3.8 37.0 - - + +
76H SER* 4.8 9.2 - - - +
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Residues in contact with ARG 21 (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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132D THR 3.0 27.0 + - - -
133D GLY* 4.0 11.7 + - - -
134D TYR 4.5 11.1 + - - -
135D CYS* 5.8 2.0 - - - +
17H LEU* 3.0 43.3 + - + +
18H THR* 4.1 6.3 - - - +
20H VAL* 1.3 74.6 - - - +
22H GLU* 1.3 57.6 + - - +
24H CYS* 3.7 1.8 - - - +
25H GLU* 3.0 41.3 + - - +
62H LEU* 5.2 2.0 - - - +
65H ARG* 3.2 59.5 - - - +
66H ASP* 4.9 2.2 + - - -
69H VAL* 4.1 9.9 - - + -
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Residues in contact with GLU 22 (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 THR* 3.2 36.5 + - + +
19H THR* 3.7 8.6 + - - +
21H ARG* 1.3 75.3 - - + +
23H GLN* 1.3 61.7 + - + +
25H GLU* 3.6 10.0 + - - +
26H GLN* 3.5 27.8 + - - +
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Residues in contact with GLN 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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19H THR* 3.2 29.8 + - + +
20H VAL* 3.3 11.4 + - - +
22H GLU* 1.3 77.2 - - + +
24H CYS* 1.3 59.5 + - - +
26H GLN* 3.4 37.5 + - - +
27H LEU* 4.2 9.2 + - - +
68H CYS* 5.0 1.5 - - - -
72H LYS* 5.4 18.5 + - + +
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Residues in contact with CYS 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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20H VAL* 2.9 23.6 + - - +
21H ARG* 3.7 6.7 - - - +
22H GLU 3.3 0.2 - - - -
23H GLN* 1.3 75.5 - - - +
25H GLU* 1.3 58.6 + - - +
26H GLN 3.3 0.9 - - - -
27H LEU* 3.3 19.9 + - - +
30H CYS* 3.4 17.6 - - - -
65H ARG* 3.6 20.4 - - + +
68H CYS* 2.0 51.6 - - + -
69H VAL* 3.2 22.2 - - - -
72H LYS* 5.1 0.9 - - - -
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Residues in contact with GLU 25 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21H ARG* 3.0 28.7 + - - +
22H GLU* 3.8 10.8 - - - +
24H CYS* 1.3 72.7 - - - +
26H GLN* 1.3 63.0 + - - +
27H LEU 3.3 2.4 + - - +
30H CYS* 4.1 9.1 - - - +
31H VAL* 3.5 20.1 + - - +
34H ARG* 2.9 39.7 + - - +
61H PHE* 3.4 24.7 - - + -
65H ARG* 3.1 28.9 + - - +
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Residues in contact with GLN 26 (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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22H GLU* 3.5 21.2 + - - +
23H GLN* 3.4 32.2 + - - +
25H GLU* 1.3 76.8 - - - +
27H LEU* 1.3 61.7 + - + +
28H GLU* 3.9 6.6 + - - +
31H VAL* 4.0 9.5 - - - +
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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