Contacts of the helix formed by residues 24 - 33 (chain D) in PDB entry 1FS1
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 SER 24 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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21D ALA 3.1 13.6 + - - +
22D LYS 3.5 0.8 - - - +
23D GLN* 1.3 78.1 - - - +
25D VAL* 1.3 64.0 + - - +
26D THR* 3.2 2.6 + - - -
27D ILE* 3.1 34.1 + - - +
28D LYS* 2.9 21.0 + - - +
62D CYS* 5.3 0.4 - - - -
110D LEU* 2.7 25.5 + - - +
112D ILE* 3.6 19.2 - - - +
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Residues in contact with VAL 25 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22D LYS 4.4 2.9 - - - +
23D GLN 3.4 5.3 + - - +
24D SER* 1.3 71.4 + - - +
26D THR* 1.3 63.5 + - + +
28D LYS* 3.3 25.6 - - + +
29D THR* 3.3 17.8 + - + +
111D ASP* 3.1 39.8 + - - +
113D LYS* 6.0 2.7 - - + +
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Residues in contact with THR 26 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24D SER* 3.2 2.4 + - - -
25D VAL* 1.3 75.2 - - + +
27D ILE* 1.3 68.8 + - - +
28D LYS 3.1 1.1 - - - -
29D THR* 2.7 24.7 + - - -
30D MET* 3.1 26.0 + - - +
109D TYR 4.4 7.1 + - - +
110D LEU* 3.2 21.3 + - - +
111D ASP* 3.9 23.1 - - + +
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Residues in contact with ILE 27 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6D LEU* 4.0 29.2 - - + -
21D ALA* 3.9 14.4 - - + +
24D SER* 3.1 28.5 + - - +
26D THR* 1.3 85.3 + - - +
28D LYS* 1.3 61.9 + - - +
30D MET* 3.1 8.8 + - - -
31D LEU* 2.8 63.0 + - + +
45D VAL* 4.4 6.5 - - + -
47D LEU* 4.1 27.6 - - + -
110D LEU* 4.2 12.1 - - + -
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Residues in contact with LYS 28 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22D LYS* 3.4 45.4 - - + +
24D SER 2.9 12.6 + - - +
25D VAL* 3.3 18.4 - - + +
26D THR 3.1 0.2 - - - -
27D ILE* 1.3 77.2 - - - +
29D THR* 1.3 62.6 + - + +
31D LEU* 4.0 4.7 - - - +
32D GLU* 2.8 75.5 + - - +
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Residues in contact with THR 29 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25D VAL* 3.3 18.8 + - + +
26D THR* 2.7 24.4 + - - -
28D LYS* 1.3 81.8 - - + +
30D MET* 1.3 61.4 + - - +
32D GLU* 5.0 0.7 - - - -
33D ASP* 2.8 50.7 + - - +
34D LEU* 3.1 4.7 + - - +
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Residues in contact with MET 30 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26D THR* 3.3 27.6 - - - +
27D ILE* 3.1 9.9 + - - +
29D THR* 1.3 85.3 + - - +
31D LEU* 1.3 53.8 + - - +
34D LEU* 3.2 29.2 + - + +
35D GLY 2.6 31.9 + - - -
36D MET* 3.2 23.0 + - + +
45D VAL* 4.2 29.2 - - + -
46D PRO* 5.5 3.8 - - - +
47D LEU* 5.8 2.0 - - - -
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Residues in contact with LEU 31 (chain D).
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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4D ILE* 3.3 33.2 - - + -
6D LEU* 4.5 0.2 - - + -
18D VAL* 4.2 24.2 - - + +
21D ALA* 3.8 17.9 - - + -
22D LYS* 4.6 1.1 - - + +
27D ILE* 2.8 44.9 + - + +
28D LYS* 4.0 7.2 - - - +
30D MET* 1.3 77.9 - - - +
32D GLU* 1.3 65.3 + - + +
35D GLY* 3.4 17.4 - - - +
36D MET 4.5 5.4 - - - +
45D VAL* 3.3 31.2 - - + -
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Residues in contact with GLU 32 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18D VAL* 6.1 3.4 - - + +
22D LYS* 3.7 14.0 - - + +
28D LYS* 2.8 56.8 + - + +
29D THR* 5.0 0.4 - - - -
31D LEU* 1.3 84.9 - - + +
33D ASP* 1.3 69.8 + - - +
35D GLY* 4.6 0.7 - - - -
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Residues in contact with ASP 33 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29D THR* 2.8 37.5 + - - +
32D GLU* 1.3 82.8 - - - +
34D LEU* 1.3 68.2 + - + +
35D GLY* 3.2 1.5 - - - -
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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