Contacts of the helix formed by residues 32 - 42 (chain A) in PDB entry 4O9U
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 32 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29A ILE 5.4 1.2 + - - -
31A HIS* 1.3 80.9 + - + +
33A PRO* 1.4 71.4 - - - +
34A LEU 3.3 2.0 - - - -
35A MET* 3.2 15.7 + - + +
36A SER* 2.8 26.7 + - - -
86A MET* 4.2 18.7 - - - +
85B VAL* 5.5 0.3 - - - +
204B PRO* 6.2 2.2 - - + -
248B MET* 3.9 20.0 - - + -
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Residues in contact with PRO 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 ILE 4.7 2.2 - - - +
30A LEU* 3.7 22.2 - - + +
31A HIS 4.0 0.2 - - - +
32A THR* 1.4 99.2 - - - +
34A LEU* 1.3 52.3 + - - +
36A SER* 3.2 3.9 + - - -
37A GLY* 2.7 29.1 + - - -
83A THR* 3.6 10.1 - - + +
86A MET* 3.7 35.9 - - + -
87A LEU* 4.2 17.3 - - + -
90A PHE* 4.4 20.2 - - + -
22B MET* 5.0 1.0 - - - +
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Residues in contact with LEU 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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23A ILE* 4.0 18.6 - - + -
26A VAL* 4.0 17.9 - - + -
30A LEU* 3.8 13.4 + - + +
31A HIS 4.8 2.0 - - - +
32A THR 3.3 0.2 - - - -
33A PRO* 1.3 77.2 - - - +
35A MET* 1.3 57.0 + - - +
37A GLY* 4.0 1.6 - - - +
38A SER* 2.8 33.9 + - - +
19B LEU* 3.5 30.3 - - + +
22B MET* 3.4 38.8 + - + +
23B ALA* 3.7 26.7 - - + -
244B LEU* 4.7 7.1 - - + +
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Residues in contact with MET 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 HIS 3.6 12.4 + - - +
32A THR* 3.2 19.6 + - + +
34A LEU* 1.3 78.7 - - - +
36A SER* 1.3 56.5 + - - +
38A SER* 3.0 8.3 + - - -
39A ASN* 3.1 10.6 + - - +
82B PRO* 5.7 1.6 - - + +
85B VAL* 3.9 23.0 - - + +
204B PRO* 4.6 2.9 - - + +
207B ILE* 3.9 28.3 - - + +
208B SER* 3.4 31.2 - - - +
211B ASN* 3.0 35.5 + - + +
244B LEU* 3.7 17.6 - - + +
248B MET* 3.8 19.1 - - + +
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Residues in contact with SER 36 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A THR 2.8 14.1 + - - -
33A PRO 3.3 8.3 - - - -
35A MET* 1.3 77.4 - - - +
37A GLY* 1.3 59.7 + - - +
39A ASN* 3.7 8.3 + - - +
40A PHE* 3.4 14.4 + - - +
79A GLY* 3.8 6.1 + - - +
82A VAL* 3.3 27.3 - - - +
83A THR* 3.1 21.6 + - - -
86A MET* 3.7 16.6 - - - -
85B VAL* 4.3 11.4 - - - +
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Residues in contact with GLY 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 PRO 2.7 18.5 + - - -
34A LEU* 3.2 5.1 + - - -
36A SER* 1.3 73.9 - - - +
38A SER* 1.3 58.4 + - - +
40A PHE* 3.3 8.1 + - - +
41A ILE* 3.1 35.6 + - - +
83A THR* 3.8 7.9 - - - -
22B MET* 4.0 20.8 - - - +
32B ILE* 4.6 1.1 - - - -
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Residues in contact with SER 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 LEU* 2.8 19.1 + - - +
35A MET* 3.0 7.4 + - - -
37A GLY* 1.3 70.7 - - - +
39A ASN* 1.3 64.2 + - - +
41A ILE* 3.2 10.9 + - - -
42A HIS* 3.1 29.0 + - - -
19B LEU* 5.3 6.5 - - - -
211B ASN* 2.7 27.9 + - - -
237B VAL* 3.3 25.7 - - - +
240B ALA* 5.2 6.1 - - - -
244B LEU* 3.8 8.7 - - - +
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Residues in contact with ASN 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 MET 3.1 14.7 + - - +
36A SER* 3.7 7.3 + - - +
38A SER* 1.3 80.3 + - - +
40A PHE* 1.3 60.9 + - - +
42A HIS* 3.0 24.5 + - - -
75A ASN* 2.8 44.9 + - - +
79A GLY* 4.6 6.6 - - - -
85B VAL* 3.3 31.2 - - + +
88B TYR* 3.6 15.1 - - - +
89B ASN* 3.1 20.7 - - - +
211B ASN* 3.3 11.2 + - - +
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Residues in contact with PHE 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 SER 3.4 5.8 + - - +
37A GLY* 3.3 12.9 + - - +
38A SER 3.2 0.2 - - - -
39A ASN* 1.3 77.4 - - - +
41A ILE* 1.3 69.8 + - + +
43A GLY* 2.9 22.5 + - - -
75A ASN 4.0 8.3 - - - -
76A ALA* 3.1 35.5 - - + +
79A GLY* 3.7 16.4 - - - +
80A TYR* 3.5 22.2 - + + -
83A THR* 4.7 1.1 - - - +
15B PHE* 5.0 1.3 - + - -
32B ILE* 4.0 13.7 - - + -
35B ALA* 3.5 39.7 - - + -
36B GLY* 4.2 9.4 - - - -
39B MET* 3.7 27.6 - - + +
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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 GLY 3.1 21.2 + - - +
38A SER* 3.2 5.8 + - - +
40A PHE* 1.3 88.3 - - + +
42A HIS* 1.3 58.2 + - - +
43A GLY 3.1 4.2 + - - -
44A VAL* 3.4 23.6 - - - +
15B PHE* 3.6 41.6 - - + +
19B LEU* 4.3 27.1 - - + -
22B MET* 4.3 15.7 - - + -
35B ALA* 4.5 4.3 - - + -
39B MET* 5.5 0.6 - - - +
233B ALA* 3.9 14.1 - - + +
236B LEU* 4.9 4.3 - - + -
237B VAL* 3.6 20.6 - - + -
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Residues in contact with HIS 42 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A SER 3.1 25.2 + - - -
39A ASN* 3.0 15.6 + - - -
41A ILE* 1.3 72.9 - - - +
43A GLY* 1.3 55.6 + - - +
44A VAL* 3.0 19.5 + - - +
45A VAL* 3.6 11.6 - - - +
75A ASN* 3.0 22.2 + - - -
89B ASN* 3.0 6.2 + - - -
92B GLY* 4.7 1.6 - - - -
211B ASN* 2.8 26.4 + - - -
214B THR* 2.9 33.5 + - + -
215B GLY* 3.9 12.1 + - - -
218B VAL* 3.9 15.4 - - + +
233B ALA 4.8 1.8 - - - +
237B VAL* 3.4 27.3 - - + +
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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