Contacts of the helix formed by residues 30 - 42 (chain A) in PDB entry 4WNB
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 ASN 30 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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27A ASP* 3.6 12.0 - - + +
28A PRO* 2.9 21.9 + - + +
29A VAL* 1.3 78.9 - - - +
31A GLN* 1.3 63.1 + - - +
32A PRO* 3.4 13.8 - - + +
33A MET* 2.9 56.7 + - - +
34A ILE* 3.1 27.6 + - - +
72A TRP* 3.7 7.2 - - - -
117A PRO* 4.7 3.6 - - - -
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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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30A ASN* 1.3 70.4 - - - +
32A PRO* 1.4 69.9 - - + +
34A ILE* 3.2 12.7 + - - +
35A ASN* 2.7 58.1 + - - +
48A TYR 2.9 23.2 + - - -
49A VAL* 3.9 7.3 + - - +
62A ILE* 3.4 35.5 - - + +
117A PRO* 4.2 10.9 - - + +
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Residues in contact with PRO 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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30A ASN* 3.4 13.9 - - + +
31A GLN* 1.4 94.3 - - + +
33A MET* 1.3 59.6 + - + +
35A ASN* 3.3 11.8 + - + +
36A ASN* 3.0 33.4 + - - +
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Residues in contact with MET 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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26A ARG* 4.0 11.4 - - - +
27A ASP* 3.5 20.4 - - - +
30A ASN* 2.9 33.8 + - - +
32A PRO* 1.3 74.7 - - + +
34A ILE* 1.3 66.1 + - - +
36A ASN* 3.4 14.6 + - - +
37A TRP* 3.1 24.3 + - - +
68A MET* 3.6 5.1 - - + +
71A VAL* 4.1 10.3 - - + +
72A TRP* 3.5 29.8 - - + -
26B ALA 5.0 2.9 - - - +
28B ARG* 3.5 31.6 - - + -
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Residues in contact with ILE 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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29A VAL* 4.4 6.7 - - + -
30A ASN 3.1 20.4 + - - +
31A GLN* 3.5 24.2 - - - +
33A MET* 1.3 76.8 - - - +
35A ASN* 1.3 58.3 + - - +
37A TRP* 3.1 2.1 + - - +
38A VAL* 2.9 33.8 + - + +
48A TYR* 3.6 35.7 - - + +
62A ILE* 4.5 0.7 - - + -
63A VAL 4.4 0.9 - - - +
64A ALA* 3.9 27.1 - - + +
65A PRO* 4.1 9.6 - - + -
68A MET* 3.9 13.2 - - - +
72A TRP* 4.0 13.0 - - + -
117A PRO* 4.4 7.4 - - + -
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Residues in contact with ASN 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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31A GLN* 2.7 55.6 + - - +
32A PRO* 3.5 10.0 - - + +
33A MET 3.2 0.2 - - - -
34A ILE* 1.3 73.2 - - - +
36A ASN* 1.3 63.9 + - - +
38A VAL* 3.5 6.7 - - - +
39A GLU* 3.0 27.9 + - - +
49A VAL* 3.8 13.3 - - - +
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Residues in contact with ASN 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 PRO* 3.0 19.6 + - - +
33A MET* 3.7 17.5 - - - +
34A ILE 3.3 0.2 - - - -
35A ASN* 1.3 77.5 - - - +
37A TRP* 1.3 56.8 + - - +
39A GLU* 3.5 19.4 - - - +
40A ALA* 3.1 29.3 + - - +
26B ALA* 3.6 15.2 - - + +
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Residues in contact with TRP 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 MET 3.1 17.2 + - - +
34A ILE 3.6 2.7 - - - +
36A ASN* 1.3 75.8 - - - +
38A VAL* 1.3 77.4 + - + +
40A ALA* 3.2 1.7 + - - +
41A ILE* 2.8 56.4 + - + +
43A ASP* 4.5 9.2 - - + -
65A PRO* 3.7 22.7 - - + -
67A ALA* 4.1 13.2 + - + -
68A MET* 3.5 30.9 - - + +
71A VAL* 4.1 6.4 - - + +
26B ALA* 3.7 26.9 - - + +
27B THR* 3.6 24.8 - - + +
53B LEU 5.0 2.3 + - - -
57B GLY* 3.6 32.8 - - - -
60B GLN* 3.7 22.4 - - - -
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Residues in contact with VAL 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 ILE* 2.9 28.6 + - + +
35A ASN* 3.5 13.2 - - - +
37A TRP* 1.3 90.6 - - + +
39A GLU* 1.3 61.1 + - + +
41A ILE* 4.6 0.2 - - - -
42A GLY* 2.8 26.5 + - - -
43A ASP 3.3 24.7 + - - +
48A TYR* 4.0 35.7 - - + -
49A VAL* 4.1 17.7 - - + -
65A PRO* 4.2 0.7 - - + -
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Residues in contact with GLU 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 ASN 3.0 20.5 + - - +
36A ASN* 3.5 20.9 - - - +
38A VAL* 1.3 81.7 - - - +
40A ALA* 1.3 65.1 + - + +
42A GLY* 3.6 6.9 + - - -
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Residues in contact with ALA 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 ASN 3.1 15.1 + - - +
37A TRP 3.9 0.4 - - - +
39A GLU* 1.3 82.2 - - + +
41A ILE* 1.3 64.9 + - + +
42A GLY* 3.4 0.9 + - - -
19B PHE* 3.8 11.3 - - - -
22B SER* 3.6 43.0 + - - +
23B THR* 3.3 18.6 - - + +
26B ALA* 3.8 8.3 - - + -
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Residues in contact with ILE 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 TRP* 2.8 56.3 + - + +
38A VAL 4.4 0.2 - - - +
40A ALA* 1.3 76.5 - - + +
42A GLY* 1.3 57.8 + - - +
43A ASP* 4.2 17.0 - - + +
19B PHE* 4.6 3.7 - - - -
23B THR* 4.0 12.3 - - + -
26B ALA* 6.0 0.4 - - + -
27B THR* 4.9 2.9 - - + -
54B THR* 3.9 40.4 - - + +
57B GLY 3.9 17.9 - - - +
58B LEU* 3.6 22.5 - - + +
61B ARG* 2.9 22.3 + - - -
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Residues in contact with GLY 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 VAL 2.8 12.2 + - - -
39A GLU 4.1 6.3 - - - -
40A ALA 3.2 3.0 - - - -
41A ILE* 1.3 79.1 - - - +
43A ASP* 1.3 60.9 + - - +
44A ARG* 3.5 18.3 + - - +
61B ARG* 3.2 24.2 + - - -
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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