Contacts of the helix formed by residues 29 - 43 (chain A) in PDB entry 2WW9
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 PHE 29 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28A PRO* 1.4 74.5 + - + +
30A ASP* 1.4 74.8 + - - +
31A ASP 3.3 0.7 - - - -
32A LYS* 3.2 7.1 + - - +
33A ILE* 3.1 49.5 + - + +
177A PHE* 3.5 29.4 - + - -
471A TYR* 5.2 5.6 - - - -
477A GLN* 3.7 32.8 - - - -
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Residues in contact with ASP 30 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28A PRO 5.2 1.4 - - - +
29A PHE* 1.4 82.3 + - - +
31A ASP* 1.4 67.1 - - - +
33A ILE* 3.2 18.8 - - - +
34A VAL* 3.2 29.3 + - + +
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Residues in contact with ASP 31 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A LEU* 3.2 48.4 - - + +
28A PRO 4.2 4.2 - - - +
29A PHE 3.3 0.4 - - - -
30A ASP* 1.4 83.4 - - - +
32A LYS* 1.4 57.1 + - - +
34A VAL* 3.4 5.2 + - - +
35A TYR* 3.0 66.0 + - + -
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Residues in contact with LYS 32 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A LYS* 5.9 1.8 - - - -
27A LEU 3.2 18.5 + - - +
28A PRO* 3.9 22.0 - - + -
29A PHE 3.2 5.1 + - - +
31A ASP* 1.4 75.2 - - - +
33A ILE* 1.4 56.0 + - - +
35A TYR 3.5 0.2 + - - -
36A THR* 3.0 31.7 + - - -
174A GLY* 3.1 38.0 + - - +
175A PHE 3.6 10.1 - - - +
176A GLY* 3.2 21.4 + - - +
177A PHE* 3.5 48.4 - - + +
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Residues in contact with ILE 33 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29A PHE* 3.1 41.1 + - + +
30A ASP* 3.2 26.0 - - - +
32A LYS* 1.4 71.8 - - - +
34A VAL* 1.4 68.2 + - + +
36A THR* 3.6 9.7 - - + +
37A ILE* 3.3 25.6 + - - +
177A PHE* 3.7 17.3 - - + -
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Residues in contact with VAL 34 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30A ASP* 3.2 20.2 + - + +
31A ASP* 3.9 5.6 - - - +
33A ILE* 1.4 80.7 - - + +
35A TYR* 1.4 69.6 + - + +
37A ILE* 3.2 11.2 - - + +
38A PHE* 3.1 34.2 + - + +
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Residues in contact with TYR 35 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A LYS* 5.4 0.9 - - - -
27A LEU* 4.9 6.5 - - + -
31A ASP* 3.0 54.1 + - + +
34A VAL* 1.4 85.3 - - + +
36A THR* 1.4 60.2 + - - +
38A PHE* 3.6 10.2 - + + +
39A ALA* 3.0 26.0 + - - +
171A ILE* 5.7 0.2 - - - +
175A PHE* 3.3 76.8 - + + +
176A GLY* 4.9 0.9 - - - -
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Residues in contact with THR 36 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32A LYS 3.0 17.2 + - - +
33A ILE* 3.6 18.4 - - + +
35A TYR* 1.4 74.1 - - - +
37A ILE* 1.4 69.0 + - + +
39A ALA* 3.6 7.6 + - - +
40A GLY* 3.3 15.9 + - - -
171A ILE* 4.2 6.5 - - - +
176A GLY* 3.7 5.5 - - - -
177A PHE* 3.5 25.9 + - + +
183A ILE* 3.2 35.6 - - + +
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Residues in contact with ILE 37 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33A ILE 3.3 12.1 + - - +
34A VAL* 3.2 21.5 - - + +
36A THR* 1.4 78.8 - - + +
38A PHE* 1.4 59.4 + - + +
40A GLY* 3.1 4.4 + - - -
41A LEU* 3.0 43.1 + - + +
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Residues in contact with PHE 38 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34A VAL* 3.1 27.1 + - + +
35A TYR* 3.6 14.1 - + + +
36A THR 3.3 0.4 - - - -
37A ILE* 1.4 73.2 - - + +
39A ALA* 1.4 58.2 + - - +
41A LEU* 3.1 35.5 + - + +
42A ILE* 3.2 21.5 + - + +
65C LEU* 3.6 37.5 - - + -
69C VAL* 5.5 4.3 - - + -
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Residues in contact with ALA 39 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35A TYR 3.0 16.4 + - - +
36A THR 3.6 6.7 - - - +
38A PHE* 1.4 75.4 - - - +
40A GLY* 1.4 57.2 + - - +
42A ILE* 3.6 6.4 + - - +
43A TYR* 3.4 19.8 + - - +
167A LEU* 3.5 36.9 - - + +
170A VAL* 5.4 2.0 - - + -
171A ILE* 3.9 27.8 - - + -
175A PHE* 6.3 0.9 - - + -
183A ILE* 6.3 0.2 - - + -
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Residues in contact with GLY 40 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36A THR 3.3 8.1 + - - -
37A ILE* 3.1 10.7 + - - -
39A ALA* 1.4 76.3 - - - +
41A LEU* 1.4 59.6 + - - +
43A TYR* 3.8 17.7 - - - -
44A LEU* 3.3 21.5 + - - +
183A ILE* 5.6 8.3 - - - +
187A VAL* 5.8 6.0 - - - +
64B ILE* 5.6 5.0 - - - +
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Residues in contact with LEU 41 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37A ILE* 3.0 32.6 + - + +
38A PHE* 3.1 33.8 + - + +
40A GLY* 1.4 76.3 - - - +
42A ILE* 1.4 61.7 + - + +
43A TYR 3.3 0.2 - - - -
44A LEU* 3.4 36.4 + - + +
45A PHE* 3.1 30.0 - - + -
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Residues in contact with ILE 42 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38A PHE* 3.2 26.4 + - + +
39A ALA* 3.6 12.5 + - - +
40A GLY 3.5 0.2 - - - -
41A LEU* 1.4 75.5 - - - +
43A TYR* 1.4 61.1 + - - +
45A PHE* 3.5 25.8 + - + +
80A LEU* 5.9 1.0 - - - +
163A PHE* 3.5 29.7 - - + -
167A LEU* 4.8 4.0 - - + -
65C LEU* 3.8 29.2 - - + -
68C SER* 3.3 29.6 - - - +
69C VAL* 5.2 7.4 - - + -
72C ILE* 3.9 15.9 - - + +
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Residues in contact with TYR 43 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39A ALA 3.4 14.7 + - - +
40A GLY* 3.8 14.6 - - - +
42A ILE* 1.4 77.2 - - - +
44A LEU* 1.4 64.8 + - + +
45A PHE 3.1 4.7 + - - -
46A ALA* 3.4 18.0 + - + +
73A GLY 4.6 0.7 - - - -
74A CYS 4.7 3.2 + - - -
75A GLU* 4.8 4.3 - - - +
80A LEU* 4.4 29.3 - - + +
163A PHE* 5.9 0.9 - - - -
167A LEU* 5.1 7.2 - - + +
184A ILE* 4.1 22.2 - - + -
187A VAL* 3.4 33.7 - - + -
188A VAL* 3.3 35.6 - - + +
191A THR* 3.0 24.5 + - - +
64B ILE* 4.4 9.0 - - + -
68B ILE* 4.5 7.1 - - + +
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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