Contacts of the helix formed by residues 30 - 42 (chain C) in PDB entry 4O9U
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 LEU 30 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26C VAL* 5.3 1.8 - - + -
27C PRO* 3.0 21.9 + - + +
29C ILE* 1.3 80.8 - - + +
31C HIS* 1.3 57.3 + - - +
32C THR 3.0 3.6 + - - -
33C PRO* 3.2 14.0 - - + +
34C LEU* 2.8 42.9 + - + +
87C LEU* 5.1 2.0 - - + -
90C PHE* 3.8 28.5 - - + -
22D MET* 3.2 25.1 - - + +
23D ALA* 3.3 18.2 - - - +
24D HIS 3.6 18.2 - - - +
25D PRO* 3.7 8.7 - - + -
28D ALA* 3.9 12.6 - - + -
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Residues in contact with HIS 31 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26C VAL* 3.7 28.3 + - + +
27C PRO 4.0 9.6 + - - -
28C VAL* 3.4 38.3 + - + +
29C ILE 3.6 0.4 - - - -
30C LEU* 1.3 76.0 - - - +
32C THR* 1.3 59.4 + - - +
34C LEU* 3.9 6.6 - - + +
35C MET* 3.1 29.5 + - - +
244D LEU* 4.9 18.9 - - + +
247D LEU* 4.9 24.4 - - + +
248D MET* 4.1 33.8 - - + +
251D ALA* 5.6 5.2 - - + -
332D PRO* 5.5 4.9 - - + +
338D PRO* 5.3 0.7 - - + -
339D GLY 5.6 2.7 - - - +
342D ASN* 5.8 0.2 - - - +
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Residues in contact with THR 32 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29C ILE 5.1 0.4 + - - -
30C LEU 3.0 1.2 + - - -
31C HIS* 1.3 72.1 - - - +
33C PRO* 1.4 74.4 - - - +
34C LEU 3.2 0.7 - - - -
35C MET* 3.0 20.7 + - + +
36C SER* 3.0 20.8 + - - -
86C MET* 3.6 21.4 - - + +
81D MET* 5.7 0.7 - - + -
82D PRO* 5.9 1.3 - - + -
85D VAL* 5.3 2.9 - - + +
337D MET* 3.9 16.2 - - - -
338D PRO 2.4 30.9 + - - +
339D GLY* 3.2 16.3 + - - -
342D ASN* 4.6 2.5 - - - +
343D VAL* 4.2 8.5 - - + -
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Residues in contact with PRO 33 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29C ILE 4.2 9.0 - - - +
30C LEU* 3.2 30.7 - - + +
32C THR* 1.4 95.7 - - - +
34C LEU* 1.3 58.3 + - - -
36C SER* 3.3 14.3 + - - -
37C GLY 3.3 8.8 + - - -
83C THR* 3.5 8.3 + - - -
86C MET* 3.5 33.0 - - + +
87C LEU* 3.8 22.2 - - + -
90C PHE* 5.0 5.6 - - + -
22D MET* 3.9 4.7 - - - +
342D ASN* 5.7 1.6 - - + -
343D VAL* 4.7 4.7 - - + -
352D TYR* 5.9 1.6 - - - +
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Residues in contact with LEU 34 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23C ILE* 4.5 20.9 - - + -
26C VAL* 4.6 16.2 - - + -
30C LEU* 2.8 34.6 + - + +
31C HIS* 3.9 4.3 - - + +
33C PRO* 1.3 71.7 - - - +
35C MET* 1.3 61.1 + - - +
37C GLY* 3.5 7.6 + - - -
38C SER* 3.6 13.1 + - - -
19D LEU* 5.0 6.1 - - + +
22D MET* 3.4 52.5 - - + +
23D ALA* 3.9 4.9 - - - +
244D LEU* 4.0 27.1 - - + +
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Residues in contact with MET 35 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31C HIS 3.1 14.0 + - - +
32C THR* 3.0 24.1 + - + +
34C LEU* 1.3 75.0 - - - +
36C SER* 1.3 62.1 + - - +
37C GLY 3.2 0.4 - - - -
38C SER* 3.0 22.2 + - - +
39C ASN* 3.2 10.7 + - - +
82D PRO* 5.2 4.0 - - + +
85D VAL* 3.6 36.3 - - + -
204D PRO 6.2 0.2 - - - +
207D ILE* 4.7 10.1 - - + -
208D SER* 5.3 7.4 - - - -
211D ASN* 4.5 4.7 + - - +
244D LEU* 4.4 20.2 - - + -
248D MET* 4.5 6.3 - - + -
337D MET* 5.7 0.4 - - - -
338D PRO* 3.3 39.9 - - + -
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Residues in contact with SER 36 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32C THR 3.0 11.1 + - - -
33C PRO* 3.3 15.0 + - - -
35C MET* 1.3 77.2 - - - +
37C GLY* 1.3 56.9 + - - +
39C ASN* 3.4 10.8 + - - +
40C PHE* 3.1 23.0 + - - +
79C GLY 3.7 3.5 - - - +
82C VAL* 3.2 30.2 - - - +
83C THR* 3.3 18.6 + - - -
86C MET* 4.8 6.3 - - - -
81D MET* 6.2 0.7 - - - -
85D VAL* 4.3 13.0 - - - +
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Residues in contact with GLY 37 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33C PRO 3.3 7.0 + - - -
34C LEU 3.5 4.0 + - - -
35C MET 3.2 1.0 - - - -
36C SER* 1.3 76.2 - - - +
38C SER* 1.3 54.1 + - - +
39C ASN 3.1 1.3 - - - -
40C PHE* 2.8 12.5 + - - +
41C ILE* 2.7 44.3 + - - +
83C THR* 4.2 7.2 + - - -
22D MET* 4.1 20.4 - - - -
32D ILE* 6.0 0.2 - - - -
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Residues in contact with SER 38 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34C LEU* 3.6 10.4 + - - -
35C MET* 3.0 17.0 + - - -
37C GLY* 1.3 74.0 - - - +
39C ASN* 1.3 52.0 + - - +
41C ILE* 3.9 15.2 - - - +
42C HIS* 2.7 37.0 + - - -
19D LEU* 5.8 5.8 - - - +
22D MET* 5.5 0.4 - - - +
211D ASN* 2.9 25.2 + - - -
237D VAL* 3.8 19.2 - - - +
240D ALA* 5.5 7.0 - - - -
241D GLY 5.8 0.4 - - - -
244D LEU* 4.6 6.0 - - - +
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Residues in contact with ASN 39 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35C MET 3.2 10.1 + - - +
36C SER* 3.4 12.6 + - - +
38C SER* 1.3 82.5 + - - +
40C PHE* 1.3 58.2 + - - +
42C HIS* 3.0 17.2 + - + -
75C ASN* 2.8 25.8 + - - -
79C GLY* 4.4 3.4 - - - -
82C VAL* 5.0 2.0 - - - +
85D VAL* 2.9 46.0 + - + +
88D TYR* 3.3 31.8 - - - +
89D ASN* 3.0 21.1 + - - +
211D ASN* 3.8 1.7 - - - +
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Residues in contact with PHE 40 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36C SER 3.1 7.0 + - - +
37C GLY* 2.8 19.5 + - - +
39C ASN* 1.3 71.3 - - - +
41C ILE* 1.3 62.7 + - + +
43C GLY* 2.8 28.2 + - - -
75C ASN 4.0 1.7 - - - +
76C ALA 3.0 28.5 - - - -
77C ALA* 5.4 0.2 - - - -
79C GLY* 3.4 24.9 - - - +
80C TYR* 3.4 38.6 - + + -
83C THR* 5.1 4.0 - - + -
15D PHE* 5.9 0.4 - + - -
32D ILE* 5.8 2.2 - - + -
35D ALA* 3.7 30.7 - - + -
36D GLY* 4.0 2.7 - - - -
39D MET* 3.3 48.8 - - + +
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Residues in contact with ILE 41 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37C GLY* 2.7 25.7 + - - +
38C SER* 3.4 16.1 + - - +
40C PHE* 1.3 80.2 - - + +
42C HIS* 1.3 56.2 + - - +
43C GLY 2.8 14.5 + - - -
44C VAL* 3.1 18.5 + - - +
15D PHE* 4.2 37.9 - - + +
19D LEU* 4.5 26.2 - - + +
22D MET* 5.2 7.6 - - - -
35D ALA* 4.4 15.7 - - + -
39D MET* 3.5 7.7 - - - +
233D ALA* 4.7 6.3 - - + -
236D LEU* 5.1 3.4 - - + -
237D VAL* 3.7 17.9 - - + -
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Residues in contact with HIS 42 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38C SER 2.7 14.5 + - - +
39C ASN* 3.0 34.8 + - - -
41C ILE* 1.3 73.6 - - - +
43C GLY* 1.3 55.7 + - - +
44C VAL* 3.0 16.3 + - - -
45C VAL* 3.4 18.4 + - - +
75C ASN* 2.7 31.8 + - - +
89D ASN* 4.0 13.3 - - - -
211D ASN* 2.8 31.5 + - - -
214D THR* 3.9 20.4 - - + +
215D GLY* 5.0 2.9 - - - -
218D VAL* 4.3 17.7 - - + +
233D ALA* 6.0 0.9 - - - -
234D GLY* 5.9 0.4 - - - -
237D VAL* 3.6 24.6 - - + +
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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