Contacts of the helix formed by residues 20 - 35 (chain K) in PDB entry 1O1F
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 20 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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162E ASP* 3.1 33.4 - - + +
163E ALA 2.4 21.5 - - - +
19K PHE* 1.3 75.0 - - - +
21K GLU* 1.3 61.7 + - - +
22K THR* 3.6 3.5 - - - -
23K GLU* 3.0 54.2 + - - +
24K ILE* 3.2 13.3 + - - +
93K PRO* 4.4 18.8 - - - +
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Residues in contact with GLU 21 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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836D PHE* 2.9 23.8 - - - +
837D MLY 4.6 2.4 - - - +
839D MLY 5.0 6.0 - - - +
840D PRO* 3.8 25.0 - - + +
159E HIS* 5.0 9.4 + - - -
160E GLY 5.0 2.3 - - - +
161E GLU* 3.5 25.5 + - - +
162E ASP 2.4 30.0 + - - +
163E ALA* 2.5 19.7 + - - +
19K PHE 4.0 0.8 + - - -
20K ASP* 1.3 69.6 - - - +
22K THR* 1.3 54.3 + - - -
24K ILE* 3.2 16.4 + - + +
25K GLU* 2.9 44.1 + - + +
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Residues in contact with THR 22 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163E ALA* 1.9 59.2 + - - +
20K ASP* 3.6 3.8 - - - -
21K GLU* 1.3 66.9 - - - +
23K GLU* 1.3 55.3 + - - +
25K GLU* 3.1 16.1 + - + +
26K ASP* 2.9 44.5 + - - +
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Residues in contact with GLU 23 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19K PHE* 3.3 27.0 - - + -
20K ASP* 3.0 45.7 + - - +
22K THR* 1.3 77.2 - - - +
24K ILE* 1.3 56.6 + - - +
26K ASP* 3.2 14.8 + - + +
27K PHE* 3.1 51.1 + - + -
88K LEU* 5.8 1.6 - - - +
91K ALA* 5.0 12.3 - - - +
93K PRO* 5.8 4.4 - - - +
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Residues in contact with ILE 24 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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837D MLY 6.0 6.5 - - + -
161E GLU* 5.5 4.5 - - - +
19K PHE* 3.9 36.6 - - + +
20K ASP 3.2 15.0 + - - +
21K GLU* 3.4 16.4 - - + +
23K GLU* 1.3 77.9 - - - +
25K GLU* 1.3 56.6 + - + +
27K PHE* 3.2 9.6 + - - +
28K LYS* 2.9 26.8 + - - +
77K PHE* 3.9 19.0 - - + -
81K LEU* 4.4 16.4 - - + -
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Residues in contact with GLU 25 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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840D PRO* 3.6 33.8 - - + +
163E ALA* 4.3 1.2 - - - +
21K GLU* 2.9 39.9 + - + +
22K THR* 3.1 19.7 + - + +
24K ILE* 1.3 77.5 - - + +
26K ASP* 1.3 58.1 + - - +
28K LYS* 3.2 19.9 + - - +
29K GLU* 3.0 41.7 + - - +
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Residues in contact with ASP 26 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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835J PHE* 4.5 23.8 - - + -
839J MLY 5.1 9.9 - - - -
22K THR* 2.9 40.6 + - - +
23K GLU* 3.2 13.1 + - + +
25K GLU* 1.3 78.3 - - - +
27K PHE* 1.3 60.0 + - + +
29K GLU* 3.2 19.2 + - - +
30K ALA* 3.0 27.7 + - - +
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Residues in contact with PHE 27 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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832J MET* 5.3 7.0 - - + -
835J PHE* 5.0 19.1 - + - -
19K PHE* 3.5 32.8 - + - -
23K GLU* 3.1 38.1 + - + -
24K ILE* 3.2 7.6 + - - +
26K ASP* 1.3 80.5 - - + +
28K LYS* 1.3 57.7 + - - +
30K ALA* 3.8 9.6 - - + +
31K PHE* 2.9 29.8 + - - +
77K PHE* 4.1 3.1 - - + -
80K PHE* 4.6 10.8 - + + -
81K LEU* 4.0 22.9 - - + -
84K PHE* 4.3 37.0 - + + -
88K LEU* 4.5 11.2 - - + -
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Residues in contact with LYS 28 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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840D PRO* 5.1 6.1 - - - -
841D LEU* 4.1 33.2 - - + +
24K ILE 2.9 12.3 + - - +
25K GLU* 3.2 27.6 + - - +
27K PHE* 1.3 76.4 - - - +
29K GLU* 1.3 78.3 + - - +
31K PHE* 3.3 6.0 + - + +
32K THR* 2.9 36.4 + - - +
77K PHE* 3.5 28.5 - - + -
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Residues in contact with GLU 29 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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842J LEU* 5.6 9.0 - - + +
25K GLU* 3.0 23.3 + - - +
26K ASP* 3.2 23.8 + - - +
28K LYS* 1.3 89.8 + - - +
30K ALA* 1.3 59.3 + - - +
32K THR* 3.2 7.9 + - - -
33K VAL* 3.0 35.2 + - + +
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Residues in contact with ALA 30 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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835J PHE* 4.7 19.3 - - + -
26K ASP 3.0 16.3 + - - +
27K PHE* 3.8 11.2 - - + +
28K LYS 3.4 0.2 - - - -
29K GLU* 1.3 75.1 - - - +
31K PHE* 1.3 62.3 + - - +
33K VAL* 3.2 8.0 + - - +
34K ILE* 3.1 38.3 + - + +
80K PHE* 4.9 5.6 - - + -
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Residues in contact with PHE 31 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27K PHE 2.9 19.1 + - - +
28K LYS* 3.4 10.8 - - + +
30K ALA* 1.3 76.1 - - - +
32K THR* 1.3 62.0 + - - +
34K ILE 3.4 0.7 + - - -
35K ASP* 2.9 37.1 + - + +
40K GLY* 3.1 43.5 - - - -
41K ILE 4.2 0.7 - - - -
42K ILE* 3.5 25.6 - - + +
75K ILE* 3.4 20.9 - - + -
76K ASN 3.5 11.0 - - - -
77K PHE* 3.6 30.3 - + + -
80K PHE* 3.7 23.1 - + + -
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Residues in contact with THR 32 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28K LYS* 2.9 22.0 + - - +
29K GLU* 3.2 8.0 + - - -
31K PHE* 1.3 83.4 - - - +
33K VAL* 1.3 64.0 + - + +
35K ASP* 3.3 23.6 - - - +
36K GLN* 4.6 1.9 - - - +
38K ALA* 6.2 4.3 - - + -
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Residues in contact with VAL 33 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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834J LEU* 5.9 2.0 - - + -
838J ILE* 5.2 7.9 - - + -
29K GLU* 3.0 19.4 + - + +
30K ALA* 3.2 7.4 + - - +
32K THR* 1.3 79.6 - - + +
34K ILE* 1.3 62.8 + - + +
36K GLN* 3.5 13.7 + - - +
50K THR* 3.4 13.2 + - + +
54K MET* 4.4 22.7 - - + -
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Residues in contact with ILE 34 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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831J TRP* 2.1 76.7 - - + -
834J LEU* 4.9 8.3 - - + -
30K ALA* 3.1 23.4 + - + +
33K VAL* 1.3 80.6 - - + +
35K ASP* 1.3 59.5 + - - +
36K GLN 3.2 2.5 + - - -
42K ILE* 3.8 15.0 - - + -
46K ASP* 3.0 25.6 - - - +
47K LEU* 3.8 10.3 - - + -
50K THR* 3.2 29.5 + - + +
80K PHE* 4.4 13.5 - - + -
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Residues in contact with ASP 35 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31K PHE* 2.9 25.9 + - + +
32K THR* 3.3 15.0 - - - +
33K VAL 3.5 0.2 - - - -
34K ILE* 1.3 74.3 - - - +
36K GLN* 1.3 56.6 + - - +
37K ASN* 2.9 25.1 - - - +
38K ALA* 3.0 21.0 + - - +
39K ASP 3.3 3.3 + - - -
40K GLY* 3.0 26.3 + - - -
41K ILE 3.1 25.9 + - - +
42K ILE* 3.5 9.7 - - + -
46K ASP* 3.2 10.4 - - - +
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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