Contacts of the helix formed by residues 34 - 45 (chain C) in PDB entry 1UU1
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 34 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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32C PRO* 3.3 5.5 - - + +
33C PHE* 1.3 98.9 - - + +
35C GLU* 1.3 61.7 + - - +
36C ASP* 3.1 11.9 - - - +
37C LEU* 2.8 47.8 + - + +
38C VAL* 3.0 10.7 + - - +
250C ILE* 4.1 20.9 - - + -
251C PHE* 3.9 11.9 - - + -
254C ARG* 3.9 16.8 - - - +
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Residues in contact with GLU 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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18B LYS* 4.2 19.1 + - - +
33C PHE 3.0 5.8 + - - -
34C PRO* 1.3 71.5 - - - +
36C ASP* 1.3 63.7 + - - +
38C VAL* 3.1 24.4 + - - +
39C ASP* 3.1 12.1 + - - +
45D LEU 5.2 0.2 - - - +
47D SER* 2.9 32.3 + - - -
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Residues in contact with ASP 36 (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 PRO* 3.7 15.9 - - - +
35C GLU* 1.3 80.1 + - - +
37C LEU* 1.3 71.2 + - - +
39C ASP* 3.3 10.6 + - + +
40C GLU* 3.0 23.6 + - - +
247C HIS* 5.7 1.0 - - - -
250C ILE* 5.8 3.6 - - - +
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Residues in contact with LEU 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 PHE* 3.5 18.2 - - + -
34C PRO* 2.8 26.6 + - + +
36C ASP* 1.3 89.0 - - - +
38C VAL* 1.3 63.7 + - - +
40C GLU* 3.2 11.1 + - - +
41C VAL* 3.2 27.0 + - - +
243C VAL* 3.8 8.6 - - + +
247C HIS* 3.6 50.5 - - + +
250C ILE* 5.1 4.7 - - + -
251C PHE* 3.6 37.5 - - + -
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Residues in contact with VAL 38 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18B LYS* 5.8 3.1 - - - +
33C PHE* 3.8 15.5 - - + -
34C PRO 3.0 14.1 + - - +
35C GLU* 3.2 21.8 - - - +
37C LEU* 1.3 77.3 - - - +
39C ASP* 1.3 58.1 + - - +
41C VAL* 3.3 4.5 + - - +
42C PHE* 3.0 26.3 + - - +
240C PHE* 4.2 10.5 - - + -
42D PHE* 3.7 25.7 - - + +
45D LEU* 4.4 16.4 - - + -
47D SER* 4.1 19.3 - - - -
50D LEU* 4.2 7.6 - - + -
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Residues in contact with ASP 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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304B ASN* 4.8 2.1 - - - +
35C GLU 3.1 8.0 + - - +
36C ASP* 3.4 13.9 - - + +
38C VAL* 1.3 81.5 - - - +
40C GLU* 1.3 59.1 + - - +
42C PHE* 3.4 9.3 + - - +
43C ARG* 2.5 70.2 + - - +
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Residues in contact with GLU 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 ASP 3.0 12.5 + - - +
37C LEU* 3.5 13.9 - - - +
38C VAL 3.2 0.4 - - - -
39C ASP* 1.3 79.1 + - - +
41C VAL* 1.3 53.4 + - - +
43C ARG* 3.3 6.2 + - - +
44C ARG* 2.8 65.7 + - + +
243C VAL* 3.9 12.7 - - + +
246C ASP* 4.1 3.5 - - - +
247C HIS* 2.9 39.1 + - - -
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Residues in contact with VAL 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 LEU 3.2 13.4 + - - +
38C VAL 3.5 7.4 - - - +
40C GLU* 1.3 75.7 - - - +
42C PHE* 1.3 54.9 + - - +
44C ARG* 3.1 4.5 + - - +
45C LEU* 2.7 38.5 + - + +
236C VAL* 4.7 4.3 - - + +
239C MET* 4.0 17.5 - - + +
240C PHE* 3.7 49.8 - - + +
243C VAL* 3.6 31.6 - - + -
42D PHE* 4.0 11.2 - - + -
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Residues in contact with PHE 42 (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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20B ASP* 5.6 0.4 - - - -
301B ARG* 2.7 56.0 + - + -
38C VAL 3.0 13.8 + - - +
39C ASP* 3.4 12.1 - - - +
41C VAL* 1.3 78.5 - - - +
43C ARG* 1.3 78.3 + - - +
45C LEU* 3.5 6.2 - - - +
38D VAL* 4.1 15.0 - - + -
39D ASP* 3.1 34.8 - - + -
42D PHE* 3.6 48.0 - + + -
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Residues in contact with ARG 43 (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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20B ASP* 2.8 31.7 + - - -
301B ARG* 2.7 51.0 + - - +
302B THR* 4.3 20.8 + - - +
304B ASN* 3.0 25.5 + - - +
39C ASP* 2.5 64.6 + - - +
40C GLU* 3.6 6.3 - - - +
42C PHE* 1.3 97.8 - - - +
44C ARG* 1.3 61.2 + - + +
45C LEU 4.0 0.3 - - - +
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Residues in contact with ARG 44 (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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40C GLU* 2.8 40.3 + - + +
41C VAL* 3.7 3.6 - - - +
43C ARG* 1.3 73.2 - - + +
45C LEU* 1.3 65.5 + - - +
46C ASN* 3.4 4.9 + - - +
60C GLU* 4.8 5.1 + - - -
64C LYS* 4.7 4.4 - - - +
235C TYR* 4.1 3.2 + - - -
239C MET* 3.6 41.3 - - + +
242C LYS* 4.1 12.1 - - - +
243C VAL* 3.3 32.9 - - - +
246C ASP* 3.0 27.4 + - - -
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Residues in contact with LEU 45 (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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298B GLU* 3.3 2.4 - - - +
301B ARG* 2.8 37.0 + - - +
41C VAL* 2.7 21.5 + - + +
42C PHE 3.5 10.8 - - - +
43C ARG 3.2 1.0 - - - +
44C ARG* 1.3 73.6 - - - +
46C ASN* 1.3 64.1 + - - +
47C SER* 3.4 22.2 - - - +
50C LEU* 4.2 8.5 - - + -
235C TYR* 3.6 17.0 - - + -
236C VAL* 4.2 17.7 - - + -
239C MET* 5.3 4.0 - - + -
38D VAL* 4.0 17.3 - - + -
42D PHE* 3.6 34.8 - - + -
240D PHE* 4.3 5.2 - - + -
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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