Contacts of the helix formed by residues 31 - 40 (chain B) in PDB entry 1UI5
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 THR 31 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29B SER 4.1 10.1 - - - +
30B THR* 1.3 75.9 - - - +
32B LEU* 1.3 64.6 + - - +
33B SER* 3.4 10.5 + - - -
34B GLU* 3.1 37.6 + - - +
35B ILE* 3.2 27.5 + - - +
53B LYS* 4.9 2.7 - - - +
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Residues in contact with LEU 32 (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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31B THR* 1.3 75.2 - - - +
33B SER* 1.3 58.0 + - - +
35B ILE* 3.2 6.4 + - + +
36B VAL* 2.9 33.2 + - - +
43B LYS* 3.9 12.1 - - - +
46B LEU* 4.2 17.9 - - + +
47B TYR* 3.1 36.1 - - + +
52B ALA* 4.7 5.2 - - - -
53B LYS* 3.7 41.4 - - + +
56B LEU* 4.1 22.7 - - + -
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Residues in contact with SER 33 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31B THR* 3.2 10.4 + - - -
32B LEU* 1.3 77.8 - - - +
34B GLU* 1.3 68.0 + - - +
36B VAL* 3.6 8.7 + - - +
37B ALA* 3.3 23.2 + - - +
43B LYS* 4.4 18.0 - - - +
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Residues in contact with GLU 34 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B LEU* 3.8 11.0 - - + +
25B ARG* 4.1 26.7 + - - +
29B SER 3.7 6.8 - - - +
30B THR* 3.5 14.2 + - - +
31B THR* 3.1 38.0 + - - +
32B LEU 3.3 0.2 - - - -
33B SER* 1.3 83.0 + - - +
35B ILE* 1.3 58.0 + - - +
37B ALA* 3.6 5.1 + - - +
38B HIS* 3.0 29.8 + - - +
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Residues in contact with ILE 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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14B ILE* 4.1 14.8 - - + +
17B ALA* 4.1 1.5 - - + +
18B ALA* 4.1 28.0 - - + +
21B LEU* 3.4 23.1 - - + -
22B PHE* 4.0 19.1 - - + -
30B THR* 3.7 14.8 - - + +
31B THR 3.2 20.2 - - - +
32B LEU* 3.2 13.0 + - + +
33B SER 3.2 0.4 - - - -
34B GLU* 1.3 76.3 - - - +
36B VAL* 1.3 59.9 + - - +
38B HIS* 3.9 0.6 - - - +
39B ALA* 2.9 33.4 + - - +
46B LEU* 4.0 17.7 - - + -
53B LYS* 5.2 0.7 - - + -
56B LEU* 4.2 10.8 - - + -
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Residues in contact with VAL 36 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32B LEU 2.9 19.5 + - - +
33B SER* 3.8 8.7 - - - +
34B GLU 3.4 0.2 - - - -
35B ILE* 1.3 76.9 - - - +
37B ALA* 1.3 59.1 + - - +
39B ALA 3.4 0.2 + - - -
40B GLY 3.1 7.8 + - - -
41B VAL* 3.0 56.2 + - + +
42B THR* 4.1 1.3 - - - +
43B LYS* 3.8 34.8 - - + +
46B LEU* 3.5 32.3 - - + -
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Residues in contact with ALA 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 SER 3.3 15.8 + - - +
34B GLU* 3.8 5.4 - - - +
36B VAL* 1.3 80.8 - - + +
38B HIS* 1.3 61.3 + - - +
40B GLY* 3.3 12.3 + - - -
41B VAL 5.2 0.2 - - - -
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Residues in contact with HIS 38 (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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17B ALA* 3.5 36.8 - - + +
20B ASP* 2.7 28.5 + - - +
21B LEU* 3.6 21.1 - - + -
24B ARG* 3.5 11.7 + - - -
34B GLU 3.0 19.3 + - - +
35B ILE 3.9 2.0 - - - +
37B ALA* 1.3 75.7 - - - +
39B ALA* 1.3 59.0 + - - +
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Residues in contact with ALA 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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13B THR* 3.5 23.7 - - + +
14B ILE* 4.0 20.4 - - + -
17B ALA* 3.8 16.4 - - + +
35B ILE 2.9 19.2 + - - +
36B VAL 3.9 3.4 - - - +
38B HIS* 1.3 78.5 - - - +
40B GLY* 1.3 59.1 - - - +
41B VAL* 3.5 19.3 + - + +
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Residues in contact with GLY 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 VAL 3.1 5.1 + - - -
37B ALA* 3.3 11.5 + - - -
38B HIS 3.4 0.8 + - - -
39B ALA* 1.3 78.4 - - - +
41B VAL* 1.3 61.3 + - - +
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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