Contacts of the helix formed by residues 34 - 45 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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32B PRO* 3.2 0.6 - - + -
33B PHE* 1.3 99.7 - - + +
35B GLU* 1.3 66.6 + - - +
36B ASP* 3.3 10.1 - - - +
37B LEU* 2.9 30.9 + - + +
38B VAL* 3.1 11.4 + - - +
250B ILE* 4.1 16.4 - - + -
251B PHE* 3.7 19.3 - - + -
254B ARG* 3.6 32.8 - - - +
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Residues in contact with GLU 35 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47A SER* 3.9 21.8 - - - +
33B PHE 3.1 3.8 + - - -
34B PRO* 1.3 72.1 - - - +
36B ASP* 1.3 62.9 + - - +
38B VAL* 3.2 4.5 + - + +
39B ASP* 3.2 33.9 + - - +
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Residues in contact with ASP 36 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34B PRO* 3.8 15.1 - - - +
35B GLU* 1.3 76.5 + - - +
37B LEU* 1.3 75.4 + - - +
38B VAL 3.4 0.2 - - - -
39B ASP* 3.5 13.9 + - - +
40B GLU* 2.9 23.0 + - - +
43B ARG* 4.3 4.6 + - - +
247B HIS* 5.7 1.0 - - - -
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Residues in contact with LEU 37 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33B PHE* 3.4 19.3 - - + -
34B PRO* 2.9 20.7 + - + +
36B ASP* 1.3 94.4 - - - +
38B VAL* 1.3 59.6 + - - +
39B ASP 3.2 0.2 - - - -
40B GLU* 3.2 7.5 + - + +
41B VAL* 2.9 33.1 + - - +
243B VAL* 3.9 17.2 - - + +
247B HIS* 3.8 50.9 - - + +
250B ILE* 5.1 4.3 - - + -
251B PHE* 3.9 26.5 - - + -
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Residues in contact with VAL 38 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A PHE* 3.7 25.1 - - + +
45A LEU* 4.3 13.5 - - + +
47A SER* 3.3 26.9 - - - +
50A LEU* 4.0 11.9 - - + -
33B PHE* 3.5 17.5 - - + +
34B PRO 3.1 13.1 + - - +
35B GLU* 3.5 7.4 - - + +
37B LEU* 1.3 75.4 - - - +
39B ASP* 1.3 56.9 + - - +
41B VAL* 3.1 4.7 + - - +
42B PHE* 2.8 32.4 + - - +
240B PHE* 4.1 13.9 - - + -
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Residues in contact with ASP 39 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42A PHE* 5.9 0.7 - - - -
35B GLU* 3.2 26.8 + - - +
36B ASP* 3.5 11.6 - - - +
38B VAL* 1.3 80.5 - - - +
40B GLU* 1.3 65.9 + - - +
42B PHE* 3.5 11.9 - - + +
43B ARG* 2.9 47.6 + - - +
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Residues in contact with GLU 40 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36B ASP 2.9 16.5 + - - +
37B LEU* 3.2 16.4 + - + +
39B ASP* 1.3 74.7 - - - +
41B VAL* 1.3 66.2 + - - +
43B ARG* 3.0 32.1 + - - +
44B ARG* 2.9 55.8 + - - +
243B VAL* 3.7 25.4 - - + -
247B HIS* 4.9 11.9 - - + -
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Residues in contact with VAL 41 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42A PHE* 4.3 7.6 - - + -
37B LEU 2.9 19.5 + - - +
38B VAL 3.1 7.8 + - - +
40B GLU* 1.3 74.0 - - - +
42B PHE* 1.3 62.5 + - - +
44B ARG* 3.2 2.9 + - - +
45B LEU* 3.1 29.7 + - + +
236B VAL* 4.6 1.8 - - + +
239B MET* 3.6 28.9 - - + +
240B PHE* 3.8 41.5 - - + -
243B VAL* 3.4 29.6 - - + -
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Residues in contact with PHE 42 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35A GLU 5.6 0.9 - - - -
38A VAL* 4.2 13.6 - - + +
39A ASP* 3.9 41.1 - - + -
42A PHE* 3.6 49.6 - + + -
43A ARG* 6.2 0.2 - - - -
38B VAL 2.8 12.2 + - - +
39B ASP* 3.5 15.3 - - + +
41B VAL* 1.3 72.4 - - - +
43B ARG* 1.3 76.9 + - + +
45B LEU* 3.3 19.9 - - - +
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Residues in contact with ARG 43 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36B ASP* 4.3 4.9 + - - +
39B ASP* 2.9 43.8 + - - +
40B GLU* 3.0 39.8 + - - +
42B PHE* 1.3 88.3 - - + +
44B ARG* 1.3 59.6 + - + +
45B LEU 3.2 7.7 - - - +
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Residues in contact with ARG 44 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40B GLU* 2.9 50.1 + - - +
41B VAL 3.2 4.0 + - - +
43B ARG* 1.3 75.8 - - + +
45B LEU* 1.3 63.2 + - - +
46B ASN* 3.3 5.4 + - - +
60B GLU* 3.6 25.3 + - - -
64B LYS* 4.8 4.4 - - - +
235B TYR* 3.7 5.7 + - - -
239B MET* 3.7 34.6 - - + +
242B LYS* 4.8 3.5 - - - +
243B VAL* 4.0 20.4 - - - +
246B ASP* 3.0 26.3 + - - -
247B HIS* 6.3 0.4 - - - -
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Residues in contact with LEU 45 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38A VAL* 5.2 11.2 - - + +
42A PHE* 4.8 8.7 - - + -
240A PHE* 5.0 4.7 - - + -
41B VAL* 3.1 20.3 + - + +
42B PHE* 3.3 18.8 - - - +
43B ARG 3.2 4.0 - - - +
44B ARG* 1.3 76.6 - - - +
46B ASN* 1.3 62.2 + - - +
47B SER* 3.4 4.7 + - - +
50B LEU* 4.2 19.1 - - + -
235B TYR* 3.4 31.6 - - + +
236B VAL* 3.9 22.9 - - + -
239B MET* 3.7 25.8 - - + -
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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