Contacts of the helix formed by residues 27 - 39 (chain B) in PDB entry 1UT8
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 GLY 27 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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25B VAL* 2.8 12.4 + - - -
26B ASP* 1.3 68.5 + - - +
28B THR* 1.3 64.0 + - - +
30B LEU 2.9 4.5 + - - -
31B GLY* 2.7 19.6 + - - -
47B TYR* 2.9 25.1 + - - -
65B VAL* 4.7 1.3 - - - -
66B LEU 2.6 25.9 + - - -
112B PHE* 3.7 6.3 - - - -
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Residues in contact with THR 28 (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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26B ASP* 3.5 2.4 + - - -
27B GLY* 1.3 71.0 - - - +
29B ASN* 1.3 63.9 + - - +
31B GLY* 3.0 2.3 + - - -
32B PHE* 2.9 52.7 + - + -
66B LEU 4.0 1.2 + - - -
67B GLY 3.9 0.3 - - - -
68B ASP* 3.0 53.2 + - + +
105B PHE* 5.0 4.7 - - + -
108B LEU* 4.0 15.7 - - + +
112B PHE* 3.4 16.5 - - - -
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Residues in contact with ASN 29 (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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26B ASP* 3.0 30.0 + - + +
28B THR* 1.3 77.7 - - - +
30B LEU* 1.3 66.7 + - - +
32B PHE* 2.8 21.5 + - - +
33B ARG* 3.0 9.9 + - - +
151B SER* 3.0 22.9 + - - -
152B THR* 3.2 39.2 + - - +
153B ASP* 3.4 17.6 - - - +
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Residues in contact with LEU 30 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B VAL* 4.4 7.6 - - + -
26B ASP 3.0 6.1 + - - +
27B GLY* 2.9 11.4 + - - +
29B ASN* 1.3 79.0 + - - +
31B GLY* 1.3 58.2 + - - +
33B ARG* 3.0 20.9 - - + +
34B PHE* 2.9 41.6 - - + -
47B TYR* 3.2 32.8 - - + +
50B THR* 4.5 2.9 - - + -
51B ILE* 3.9 26.2 - - + -
54B LEU* 5.8 0.4 - - + -
150B ILE* 5.1 6.7 + - + +
169B PHE* 3.4 44.4 - - + -
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Residues in contact with GLY 31 (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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27B GLY 2.7 13.2 + - - -
28B THR 3.3 5.2 - - - -
29B ASN 3.0 0.6 + - - -
30B LEU* 1.3 78.4 - - - +
32B PHE* 1.3 60.2 + - - +
33B ARG 3.4 0.2 + - - -
34B PHE* 3.5 5.9 + - - +
35B LYS 3.3 10.7 + - - -
43B PHE* 3.9 6.8 - - - -
47B TYR* 3.7 8.2 - - - -
104B PHE* 3.2 18.9 - - - -
108B LEU* 3.8 21.3 - - - -
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Residues in contact with PHE 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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28B THR* 2.9 46.5 + - + -
29B ASN* 2.8 9.6 + - - +
31B GLY* 1.3 73.2 - - - +
33B ARG* 1.3 65.9 + - - +
35B LYS* 3.0 28.0 + - + -
36B HIS* 2.7 50.3 + + + +
101B ASP* 5.5 0.9 - - - -
104B PHE* 3.3 28.5 - + - -
105B PHE* 3.7 17.0 - + - -
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Residues in contact with ARG 33 (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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29B ASN* 3.0 8.0 + - - +
30B LEU* 3.0 24.7 - - + +
32B PHE* 1.3 81.0 - - - +
34B PHE* 1.3 61.2 + - + +
36B HIS* 3.0 38.0 + - - +
37B ASN* 2.6 61.2 + - - +
152B THR* 4.5 5.4 - - - -
169B PHE* 3.6 41.5 + - + +
170B THR* 3.6 31.3 + - - +
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Residues in contact with PHE 34 (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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30B LEU* 2.9 41.3 + - + -
31B GLY 3.8 5.4 - - - +
33B ARG* 1.3 78.5 - - + +
35B LYS* 1.3 57.0 + - - +
36B HIS 3.2 0.2 - - - -
37B ASN* 3.2 22.7 - - + +
38B ASN* 2.7 37.5 + - - +
43B PHE* 3.8 32.1 - + + -
46B SER* 3.4 20.9 - - - -
47B TYR* 3.4 39.5 - + - -
50B THR* 3.6 24.5 - - + -
169B PHE* 6.3 0.7 - + - -
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Residues in contact with LYS 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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31B GLY 3.3 8.0 + - - +
32B PHE* 3.0 38.3 + - + +
34B PHE* 1.3 77.9 - - - +
36B HIS* 1.3 69.3 + - + +
38B ASN* 3.4 0.3 + - - -
39B SER* 2.8 54.8 + - - +
43B PHE* 5.3 2.0 - - - -
93B ARG* 6.0 0.9 - - - +
100B LEU* 4.3 10.7 + - - +
101B ASP* 2.9 31.8 + - - +
104B PHE* 3.5 42.3 - - + +
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Residues in contact with HIS 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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32B PHE* 2.7 53.5 + + + +
33B ARG* 3.4 29.2 + - - +
35B LYS* 1.3 85.6 - - + +
37B ASN* 1.3 62.2 + - - +
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Residues in contact with ASN 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 ARG* 2.6 44.9 + - - +
34B PHE* 3.1 37.3 + - + +
36B HIS* 1.3 81.3 - - - +
38B ASN* 1.3 65.1 + - + +
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Residues in contact with ASN 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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34B PHE* 2.7 17.1 + - - +
35B LYS 3.4 0.4 + - - -
37B ASN* 1.3 79.5 - - + +
39B SER* 1.3 57.5 + - - +
40B LYS* 3.0 14.9 + - - +
41B LYS* 2.7 65.3 + - - +
43B PHE* 5.3 2.1 - - - -
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Residues in contact with SER 39 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35B LYS* 2.8 53.3 + - - +
38B ASN* 1.3 68.7 - - - +
40B LYS* 1.3 86.8 + - - +
41B LYS 3.6 1.1 - - - -
43B PHE* 6.3 2.2 - - - -
100B LEU* 3.6 9.6 - - - +
103B GLN* 3.2 16.8 + - - +
104B PHE* 5.4 6.0 - - - +
107B TYR* 5.1 3.7 - - - -
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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