Contacts of the helix formed by residues 30 - 44 (chain B) in PDB entry 4L9T
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 30 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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24B LEU* 4.5 3.0 - - - +
29B ILE* 1.3 78.5 - - - +
31B ASN* 1.3 59.9 + - - +
32B GLU* 3.6 7.1 + - - +
33B GLN* 2.9 45.2 + - - +
34B GLY* 2.9 25.6 + - - -
67B LEU* 5.2 0.2 - - - +
201B SO4 3.9 17.9 - - - +
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Residues in contact with ASN 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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17B LYS* 4.6 10.7 - - - +
21B ASP* 4.2 11.3 + - - -
24B LEU* 3.7 27.7 - - + +
30B THR* 1.3 72.7 - - - +
32B GLU* 1.3 59.2 + - - +
34B GLY* 3.2 2.6 + - - -
35B HIS* 2.9 29.1 + - - +
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Residues in contact with GLU 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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30B THR* 3.3 7.0 + - - +
31B ASN* 1.3 78.6 + - - +
33B GLN* 1.3 59.9 + - - +
35B HIS* 3.3 9.3 + - - +
36B THR* 2.9 31.9 + - - -
57B LEU* 4.3 18.4 - - + +
59B ARG* 2.4 59.9 + - + +
67B LEU* 3.5 20.6 - - + -
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Residues in contact with GLN 33 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28B ASP 4.2 2.1 - - - +
29B ILE* 3.3 17.9 - - + +
30B THR* 2.9 49.0 + - - +
32B GLU* 1.3 74.1 - - - +
34B GLY* 1.3 57.9 + - - +
36B THR* 3.2 2.6 + - - -
37B LEU* 2.9 35.7 + - - +
67B LEU* 3.8 28.0 - - + +
70B ASN* 3.1 40.1 + - - +
71B LEU* 4.0 18.3 - - + +
74B LYS* 5.1 0.3 + - - -
201B SO4 5.4 0.2 + - - -
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Residues in contact with GLY 34 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B LEU* 4.6 8.5 - - - -
29B ILE* 4.1 17.9 - - - +
30B THR 2.9 14.1 + - - -
31B ASN 3.2 4.2 + - - -
33B GLN* 1.3 77.3 - - - +
35B HIS* 1.3 55.6 + - - +
37B LEU* 3.4 4.4 + - - +
38B GLY* 2.9 26.7 + - - -
101B VAL* 5.4 0.7 - - - +
104B PHE* 6.4 1.1 - - - -
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Residues in contact with HIS 35 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31B ASN* 2.9 16.8 + - - +
32B GLU* 3.3 15.0 + - - +
34B GLY* 1.3 76.7 - - - +
36B THR* 1.3 57.7 + - - +
38B GLY* 5.0 1.3 - - - -
39B TYR* 3.0 32.7 + - + +
56B ALA* 4.2 13.9 + - - +
57B LEU* 3.4 25.4 + - + +
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Residues in contact with THR 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 GLU 2.9 14.4 + - - -
33B GLN 3.5 7.9 - - - -
34B GLY 3.2 0.2 - - - -
35B HIS* 1.3 74.7 - - - +
37B LEU* 1.3 66.1 + - - +
39B TYR* 3.3 5.1 + - - +
40B LEU* 3.1 30.2 + - + +
53B ILE* 4.1 20.6 - - + -
57B LEU* 3.1 24.3 - - - +
67B LEU* 3.2 27.4 - - + +
68B LEU* 4.3 10.8 - - + -
71B LEU* 3.8 10.5 - - + -
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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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29B ILE* 4.2 13.9 - - + -
33B GLN 2.9 20.0 + - - +
34B GLY* 3.8 3.6 - - - +
36B THR* 1.3 76.4 - - - +
38B GLY* 1.3 56.8 + - - +
40B LEU* 3.4 4.0 + - + +
41B TYR* 2.9 28.6 + - - +
71B LEU* 3.8 30.7 - - + -
76B LEU* 4.2 13.0 - - + -
77B ILE* 4.0 9.4 - - + -
93B LEU* 3.5 27.7 - - + +
97B GLY* 4.9 1.6 - - - +
100B LEU* 4.0 29.6 - - + -
101B VAL* 3.5 22.2 - - + +
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Residues in contact with GLY 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 GLY 2.9 16.4 + - - -
35B HIS* 3.9 3.1 - - - -
36B THR 3.2 0.2 - - - -
37B LEU* 1.3 76.4 - - - +
39B TYR* 1.3 60.9 + - - +
41B TYR* 3.3 10.2 + - - +
42B ALA* 3.1 23.2 + - - +
101B VAL* 4.2 11.2 - - - +
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Residues in contact with TYR 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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35B HIS* 3.0 27.1 + - + +
36B THR* 3.7 4.5 - - - +
37B LEU 3.3 0.2 - - - -
38B GLY* 1.3 73.2 - - - +
40B LEU* 1.3 63.7 - - - +
42B ALA* 3.1 2.6 + - - -
43B HIS* 3.0 60.6 + + + +
48B LEU* 3.7 27.7 - - + +
52B ASP* 4.0 12.2 + - - +
53B ILE* 3.5 37.7 - - + -
56B ALA* 3.5 31.8 - - + +
57B LEU* 5.3 2.9 - - + -
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Residues in contact with LEU 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 THR* 3.1 31.2 + - + +
37B LEU* 3.6 7.2 - - - +
39B TYR* 1.3 73.9 - - - +
41B TYR* 1.3 62.6 + - - +
44B GLN* 2.9 33.9 + - + +
48B LEU* 3.8 17.5 - - + -
53B ILE* 3.6 26.2 - - + -
68B LEU* 5.0 2.0 - - + -
77B ILE* 3.6 31.4 - - + -
91B ILE* 3.9 33.0 - - + +
92B GLY 4.9 0.9 - - - +
93B LEU* 3.8 18.4 - - + +
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Residues in contact with TYR 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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37B LEU 2.9 18.5 + - - +
38B GLY 3.4 8.1 - - - +
39B TYR 3.2 0.2 - - - -
40B LEU* 1.3 76.4 - - - +
42B ALA* 1.3 64.4 + - + +
44B GLN* 4.7 9.0 + - - +
45B GLN* 5.0 1.2 - - - +
93B LEU* 3.6 19.7 - - + +
98B ILE* 4.0 16.6 - - + -
101B VAL* 3.7 27.4 - - + -
102B GLU* 2.6 44.6 + - + +
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Residues in contact with ALA 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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38B GLY 3.1 14.8 + - - +
39B TYR* 3.1 1.3 + - - -
41B TYR* 1.3 82.1 - - + +
43B HIS* 1.3 84.4 + - + +
45B GLN* 3.4 16.7 + - - +
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Residues in contact with HIS 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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39B TYR* 3.0 53.9 + + + +
42B ALA* 1.3 97.4 + - + +
44B GLN* 1.3 65.2 + - - +
45B GLN* 3.0 16.6 + - - +
46B ASP* 3.0 27.2 + - - +
48B LEU* 3.5 19.7 - - + +
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Residues in contact with GLN 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 LEU* 2.9 22.4 + - + +
41B TYR* 4.7 8.1 + - - +
43B HIS* 1.3 71.3 - - - +
45B GLN* 1.3 65.5 + - - +
46B ASP 2.9 7.2 + - - -
47B GLY* 3.3 12.0 + - - -
48B LEU* 3.8 11.1 + - + +
78B TYR* 4.7 3.8 + - - -
91B ILE 4.4 13.0 - - - +
92B GLY* 3.4 6.7 - - - -
93B LEU* 2.8 51.4 + - - +
98B ILE* 4.3 14.3 - - - +
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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