Contacts of the helix formed by residues 28 - 43 (chain A) in PDB entry 4WAA
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 28 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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27A ARG* 1.3 76.1 - - - +
29A PHE* 1.3 64.1 + - - +
30A GLU* 3.5 6.6 + - - +
31A GLN* 2.9 40.9 + - - +
32A ARG* 3.0 24.0 + - - +
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Residues in contact with PHE 29 (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 THR* 1.3 72.9 - - - +
30A GLU* 1.3 78.7 + - + +
32A ARG* 3.1 33.3 + - - +
33A VAL* 2.9 50.7 + - + +
120A ASP* 4.9 1.3 - - - -
121A GLU* 4.1 22.2 - - + -
122A ASP* 3.8 23.1 - - + -
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Residues in contact with GLU 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 THR* 3.3 6.5 + - - +
29A PHE* 1.3 96.5 - - + +
31A GLN* 1.3 64.8 + - - +
33A VAL* 3.8 16.6 - - - +
34A GLU* 3.0 24.6 + - - +
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Residues in contact with GLN 31 (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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26A ARG 4.3 2.6 - - - +
27A ARG* 3.4 43.6 + - + +
28A THR* 2.9 50.5 + - + +
30A GLU* 1.3 76.8 - - - +
32A ARG* 1.3 56.9 + - - +
34A GLU* 3.5 5.9 + - - +
35A ASP* 2.9 35.2 + - - +
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Residues in contact with ARG 32 (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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23A PHE* 3.6 24.7 - - + -
24A LYS* 3.7 35.7 + - - +
27A ARG* 3.1 32.8 + - + -
28A THR* 3.0 7.8 + - - +
29A PHE* 3.3 42.7 - - - +
31A GLN* 1.3 75.6 - - - +
33A VAL* 1.3 60.2 + - - +
35A ASP* 3.1 5.9 + - - +
36A VAL* 2.9 34.7 + - - +
120A ASP* 4.7 0.6 + - - -
122A ASP* 2.7 52.2 + - + +
124A PHE* 3.4 6.1 - - + -
126A TYR* 3.4 11.7 - - - -
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Residues in contact with VAL 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* 2.9 51.5 + - + +
30A GLU* 3.8 17.0 - - - +
32A ARG* 1.3 74.3 - - - +
34A GLU* 1.3 62.9 + - - +
36A VAL* 3.4 2.6 + - - +
37A ARG* 3.1 21.9 + - + +
121A GLU 5.1 1.3 - - - +
122A ASP* 4.0 17.9 + - - +
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Residues in contact with GLU 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 GLU 3.0 18.6 + - - +
31A GLN* 3.7 7.4 - - - +
33A VAL* 1.3 77.5 - - - +
35A ASP* 1.3 67.4 + - - +
37A ARG* 2.3 44.5 + - - -
38A LEU* 3.2 38.0 + - + +
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Residues in contact with ASP 35 (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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23A PHE* 4.2 9.7 - - - -
27A ARG* 2.7 48.4 + - - -
31A GLN 2.9 25.6 + - - +
32A ARG* 3.1 10.7 + - - +
34A GLU* 1.3 77.9 - - - +
36A VAL* 1.3 56.8 + - - +
38A LEU* 3.4 13.8 + - - +
39A ILE* 3.0 38.6 + - + +
67A LYS* 5.5 1.9 + - - -
124A PHE* 3.7 15.3 - - + -
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Residues in contact with VAL 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 ARG 2.9 13.2 + - - +
33A VAL 3.8 5.4 - - - +
35A ASP* 1.3 72.8 - - - +
37A ARG* 1.3 66.7 + - - +
39A ILE* 4.4 4.3 - - - -
40A ARG* 2.9 60.6 + - + +
48A PRO* 4.9 4.9 - - + -
122A ASP 3.2 17.9 - - - +
123A GLY* 3.8 16.4 - - - +
124A PHE* 3.2 40.6 - - + -
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Residues in contact with ARG 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 VAL* 3.1 13.9 + - + +
34A GLU* 2.3 62.2 + - - +
36A VAL* 1.3 78.4 - - - +
38A LEU* 1.3 87.0 + - - +
40A ARG* 3.3 7.6 + - - +
41A GLU* 2.9 47.4 + - - +
113B GLU* 3.0 24.7 - - + +
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Residues in contact with LEU 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 GLU* 3.2 32.4 + - + +
35A ASP* 3.6 15.0 - - - +
37A ARG* 1.3 98.0 - - - +
39A ILE* 1.3 59.2 + - + +
41A GLU* 3.0 9.9 + - - +
42A GLN* 2.8 55.2 + - - +
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Residues in contact with ILE 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 ASP* 3.0 26.6 + - + +
36A VAL* 3.9 3.1 - - - +
38A LEU* 1.3 76.2 - - + +
40A ARG* 1.3 59.7 + - - +
42A GLN* 4.4 6.5 - - - +
43A HIS* 2.8 42.4 + - + +
46A LYS 5.7 1.1 - - - +
48A PRO* 3.9 23.6 - - + -
67A LYS* 6.2 4.3 - - - -
69A LEU* 3.8 31.6 - - + -
124A PHE* 4.0 25.4 - - + -
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Residues in contact with ARG 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 VAL* 2.9 40.7 + - + +
37A ARG* 3.7 6.1 - - - +
39A ILE* 1.3 80.5 - - + +
41A GLU* 1.3 60.7 + - - +
43A HIS 4.5 4.7 - - - -
44A PRO* 3.3 24.6 - - - +
46A LYS 6.0 1.1 - - - +
48A PRO* 5.6 6.0 - - + +
115A TYR* 2.6 30.1 + - - -
119A LYS* 4.8 3.2 - - - +
123A GLY* 4.0 11.5 - - - -
110B PRO* 3.8 7.6 - - - +
112B SER* 4.5 3.5 + - - +
113B GLU* 4.4 32.3 + - + +
116B GLU* 3.6 39.2 + - - +
117B SER* 5.7 1.2 + - - -
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Residues in contact with GLU 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 ARG* 2.9 44.2 + - - +
38A LEU* 3.0 6.4 + - - +
40A ARG* 1.3 77.1 - - - +
42A GLN* 1.3 65.9 + - + +
43A HIS 3.6 0.2 + - - -
44A PRO* 3.7 8.5 - - - +
109B THR* 3.4 16.1 - - - +
110B PRO* 3.9 20.6 - - + +
113B GLU* 2.8 31.7 - - - +
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Residues in contact with GLN 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 LEU* 2.8 51.9 + - - +
39A ILE* 4.0 5.4 - - - +
41A GLU* 1.3 81.9 - - + +
43A HIS* 1.3 86.9 + - + +
44A PRO* 3.6 4.4 - - - +
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Residues in contact with HIS 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 ILE* 2.8 23.8 + - + +
40A ARG* 3.7 5.2 - - - +
42A GLN* 1.3 106.1 + - + +
44A PRO* 1.3 67.4 - - - +
45A THR* 3.1 5.4 + - - -
46A LYS* 3.2 45.7 + - + +
69A LEU* 3.5 35.5 - - + +
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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