Contacts of the helix formed by residues 31 - 46 (chain B) in PDB entry 5WWT
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 31 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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27B VAL* 2.6 29.0 + - - -
28B THR 4.6 0.4 + - - -
30B LEU* 1.3 72.4 - - - +
32B LYS* 1.3 64.9 + - - -
33B GLN* 3.3 3.8 - - - -
34B GLU 3.1 11.8 + - - -
35B ALA* 3.1 13.9 + - - +
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Residues in contact with LYS 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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22B MET* 3.6 25.5 - - + +
27B VAL* 4.2 28.1 - - + +
31B GLY* 1.3 70.3 - - - -
33B GLN* 1.3 61.5 + - + +
35B ALA* 4.7 1.3 - - - +
36B GLU* 2.9 42.6 + - - +
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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
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31B GLY 3.3 1.7 - - - -
32B LYS* 1.3 79.7 - - + +
34B GLU* 1.3 60.6 + - + +
36B GLU* 4.5 8.2 - - - +
37B ARG* 3.9 16.6 + - - +
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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
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30B LEU* 3.5 45.6 - - + +
31B GLY 3.1 1.4 + - - -
32B LYS 3.1 0.6 - - - -
33B GLN* 1.3 78.1 - - + +
35B ALA* 1.3 67.2 + - - +
36B GLU 3.1 1.8 - - - -
37B ARG* 2.1 48.0 + - - +
38B LYS* 2.9 31.6 + - - +
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Residues in contact with ALA 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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21B PHE* 4.1 6.7 - - - +
22B MET* 3.8 18.0 - - - +
26B ILE* 3.9 29.8 - - + +
27B VAL* 5.2 1.8 - - + +
30B LEU* 4.7 7.7 - - + +
31B GLY 3.1 14.4 + - - +
32B LYS* 4.2 1.8 - - - +
34B GLU* 1.3 78.8 + - - +
36B GLU* 1.3 57.8 + - - +
38B LYS* 3.2 10.0 + - - +
39B PHE* 2.9 28.8 + - - +
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Residues in contact with GLU 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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18B LYS* 5.5 10.1 + - + -
22B MET* 3.5 23.0 - - + -
32B LYS* 2.9 23.6 + - - +
33B GLN* 4.5 8.8 - - - +
35B ALA* 1.3 77.6 - - - +
37B ARG* 1.3 56.8 + - - +
39B PHE* 3.2 7.3 + - + +
40B GLU* 2.9 46.8 + - + +
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Residues in contact with ARG 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 GLN 3.9 11.3 + - - +
34B GLU* 2.1 42.3 + - - +
36B GLU* 1.3 76.1 - - - +
38B LYS* 1.3 58.2 + - - +
40B GLU* 3.9 7.1 - - + +
41B THR* 2.5 50.2 + - - +
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Residues in contact with LYS 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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21B PHE* 5.9 5.4 - - + -
30B LEU* 5.8 6.1 - - + -
34B GLU* 2.9 21.9 + - - +
35B ALA* 3.3 13.9 - - - +
37B ARG* 1.3 79.6 - - - +
39B PHE* 1.3 56.8 + - - +
41B THR* 3.3 5.3 + - - -
42B LEU* 2.9 29.0 + - - +
425B ASP* 3.7 10.4 + - - +
427B SER* 3.5 38.8 + - - +
428B ALA* 4.5 7.1 + - - +
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Residues in contact with PHE 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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14B GLU* 3.6 13.9 - - + -
17B LEU* 3.5 33.0 - - + -
18B LYS* 3.5 35.0 - - + -
21B PHE* 3.6 37.8 - + + +
22B MET* 5.2 3.4 - - + -
35B ALA 2.9 12.6 + - - +
36B GLU* 3.4 12.3 - - + +
38B LYS* 1.3 76.8 - - - +
40B GLU* 1.3 74.0 + - - +
42B LEU* 3.2 12.4 + - + +
43B LEU* 2.9 61.9 + - + +
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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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6B LYS* 3.2 30.8 + - - +
14B GLU* 4.5 2.1 - - - +
36B GLU* 2.9 34.2 + - + +
37B ARG* 3.9 6.5 - - + +
39B PHE* 1.3 92.5 - - - +
41B THR* 1.3 58.6 + - - +
43B LEU* 3.3 5.7 + - - +
44B LYS* 2.9 29.2 + - - +
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Residues in contact with THR 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 ARG* 2.5 37.2 + - - +
38B LYS* 3.5 7.1 - - - -
40B GLU* 1.3 73.2 - - - +
42B LEU* 1.3 59.9 + - - +
44B LYS* 3.2 6.5 + - + +
45B HIS* 2.8 59.3 + - + -
427B SER* 4.0 17.0 - - - +
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Residues in contact with LEU 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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17B LEU* 6.4 0.2 - - + -
21B PHE* 3.4 42.8 - - + -
38B LYS 2.9 14.4 + - - +
39B PHE* 3.2 16.2 - - + +
41B THR* 1.3 75.7 - - - +
43B LEU* 1.3 66.9 + - + +
45B HIS* 3.0 12.7 + - - +
46B LEU* 3.0 29.4 + - + +
375B ILE* 3.7 19.1 - - + -
425B ASP* 4.6 4.0 - - - +
426B PRO* 3.8 37.5 - - + -
427B SER* 3.7 14.5 - - - +
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Residues in contact with LEU 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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6B LYS* 3.4 20.8 - - - +
7B ILE* 3.2 50.1 + - + +
9B LEU* 3.9 13.9 - - + -
14B GLU* 3.6 28.5 - - + +
17B LEU* 4.7 5.8 - - + -
39B PHE* 2.9 52.1 + - + +
40B GLU* 3.7 9.4 - - - +
42B LEU* 1.3 80.9 - - + +
44B LYS* 1.3 60.3 + - - +
45B HIS 3.6 0.2 + - - -
46B LEU* 3.9 14.1 + - + -
47B SER* 3.9 2.8 + - - -
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Residues in contact with LYS 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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2B SER* 2.8 40.3 + - - +
4B PHE 3.1 22.5 + - - +
5B PRO* 4.4 5.4 - - - -
6B LYS* 4.0 18.4 - - + +
40B GLU 2.9 16.7 + - - +
41B THR* 3.5 8.3 - - - +
42B LEU 3.1 0.2 - - - -
43B LEU* 1.3 78.2 - - - +
45B HIS* 1.3 66.0 + - + +
47B SER* 4.0 4.0 + - - -
48B HIS* 3.1 24.4 + - - -
431B LEU* 4.5 2.0 - - + +
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Residues in contact with HIS 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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41B THR* 2.8 47.9 + - + +
42B LEU 3.0 4.7 + - - +
44B LYS* 1.3 80.4 - - + +
46B LEU* 1.3 63.7 + - - +
47B SER 3.1 4.5 + - - -
48B HIS* 3.1 12.3 + - - +
332B ARG* 3.3 18.7 + - - -
426B PRO* 3.1 38.4 - - + +
427B SER* 4.4 1.8 - - - -
429B VAL 3.1 21.1 + - - -
430B PRO* 3.9 4.2 - - + +
431B LEU* 3.5 46.5 + - + +
454B ASP* 4.8 2.0 - - - -
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Residues in contact with LEU 46 (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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7B ILE* 4.2 27.1 - - + -
42B LEU* 3.0 27.0 + - + +
43B LEU* 4.2 12.6 - - + +
44B LYS 3.5 0.8 - - - -
45B HIS* 1.3 76.6 - - - +
47B SER* 1.3 58.8 + - - +
48B HIS 3.2 0.6 + - - -
329B MET* 3.7 29.4 - - + +
330B GLY* 4.3 5.2 - - - +
331B GLN 3.9 4.6 - - - +
332B ARG* 3.9 24.8 - - + +
333B PRO* 3.6 3.5 - - - +
334B ASN* 2.8 29.0 + - + +
375B ILE* 4.2 17.3 - - + -
426B PRO* 3.9 21.8 - - + -
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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