Contacts of the helix formed by residues 33 - 46 (chain s) in PDB entry 6FF7
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 ALA 33 (chain s).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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29s TRP 3.1 13.1 + - - +
30s SER 3.5 2.9 - - - +
32s GLU* 1.3 81.0 - - + +
34s PRO* 1.3 64.0 - - - +
35s LYS 3.6 1.3 - - - -
36s ALA* 4.5 8.1 - - + -
37s CYS* 3.3 22.7 + - - +
86s GLU* 4.7 18.6 - - + +
128s THR* 6.1 1.1 - - - -
129s ILE 4.1 11.4 - - - +
130s PHE* 4.1 22.4 - - + -
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Residues in contact with PRO 34 (chain s).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30s SER* 3.4 15.4 - - - +
31s LYS 4.5 4.6 - - - +
33s ALA* 1.3 74.0 - - - +
35s LYS* 1.3 59.1 + - - +
37s CYS* 3.9 1.4 - - + +
38s ARG* 2.9 30.4 + - - +
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Residues in contact with LYS 35 (chain s).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33s ALA 3.6 0.4 - - - -
34s PRO* 1.3 76.7 - - - +
36s ALA* 1.3 61.0 + - - +
38s ARG* 3.3 7.2 + - - +
39s ASN* 2.9 29.1 + - - +
83s PHE* 5.0 17.0 - - + -
84s LYS 6.1 1.1 - - - +
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Residues in contact with ALA 36 (chain s).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33s ALA* 4.1 9.3 + - + +
34s PRO 3.5 0.4 - - - -
35s LYS* 1.3 76.3 - - - +
37s CYS* 1.3 60.4 + - - +
39s ASN* 3.4 6.5 + - - +
40s PHE* 2.9 28.6 + - - +
86s GLU* 6.0 2.7 - - + -
101s MET* 5.6 7.9 - - + -
128s THR* 5.0 14.8 - - - +
130s PHE* 4.0 20.2 - - + -
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Residues in contact with CYS 37 (chain s).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28s LEU* 4.5 17.0 - - + -
29s TRP 4.5 2.7 - - - +
30s SER* 4.2 20.4 - - - -
33s ALA 3.3 19.8 + - - +
34s PRO 4.1 1.6 - - - +
35s LYS 3.4 0.2 - - - -
36s ALA* 1.3 75.8 - - - +
38s ARG* 1.3 61.3 + - - +
40s PHE* 3.7 6.5 - - - +
41s ILE* 2.9 31.2 + - - +
130s PHE* 4.5 8.6 - - + +
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Residues in contact with ARG 38 (chain s).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34s PRO 2.9 21.0 + - - +
35s LYS* 3.4 9.0 - - - +
37s CYS* 1.3 78.3 - - - +
39s ASN* 1.3 55.9 + - - +
41s ILE* 3.9 3.2 - - - +
42s GLN* 2.9 31.6 + - - +
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Residues in contact with ASN 39 (chain s).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35s LYS 2.9 17.4 + - - +
36s ALA* 3.7 6.3 - - - +
38s ARG* 1.3 75.3 - - - +
40s PHE* 1.3 57.9 + - - +
42s GLN* 3.7 5.9 - - - +
43s LEU* 2.9 31.9 + - - +
77s SER* 5.4 12.3 - - - -
78s ILE* 5.6 7.5 - - + +
110s GLY 5.2 10.1 - - - +
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Residues in contact with PHE 40 (chain s).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36s ALA 2.9 17.5 + - - +
37s CYS* 3.7 8.1 - - - +
38s ARG 3.2 0.2 - - - -
39s ASN* 1.3 77.9 - - - +
41s ILE* 1.3 57.7 + - - +
43s LEU* 3.4 4.5 + - - +
44s CYS* 2.9 28.3 + - - +
130s PHE* 6.5 0.7 - - + -
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Residues in contact with ILE 41 (chain s).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37s CYS 2.9 16.4 + - - +
38s ARG* 4.3 3.8 - - - +
40s PHE* 1.3 76.5 - - - +
42s GLN* 1.3 57.8 + - - +
44s CYS* 3.8 7.3 - - - +
45s LEU* 2.9 30.3 + - - +
169s ASN* 6.3 4.9 - - + -
170s PRO 6.1 0.9 - - - +
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Residues in contact with GLN 42 (chain s).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38s ARG 2.9 19.5 + - - +
39s ASN* 3.7 6.7 - - - +
40s PHE 3.3 0.2 - - - -
41s ILE* 1.3 76.8 - - - +
43s LEU* 1.3 57.4 + - - +
45s LEU* 3.2 6.1 + - - +
46s GLU* 2.9 29.7 + - - +
78s ILE* 5.0 16.4 - - + -
173s ASP* 5.5 12.8 - - + -
174s ILE 5.7 4.5 - - - +
175s ILE* 5.7 2.3 - - - -
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Residues in contact with LEU 43 (chain s).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39s ASN 2.9 17.6 + - - +
40s PHE* 4.1 3.8 - - - +
42s GLN* 1.3 74.1 - - - +
44s CYS* 1.3 61.5 + - - +
46s GLU* 3.9 2.7 - - - -
47s ALA 3.8 0.5 + - - -
48s TYR* 3.1 44.4 + - + +
49s TYR* 4.1 5.2 + - + +
111s SER* 5.7 9.4 - - - -
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Residues in contact with CYS 44 (chain s).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15s VAL* 5.4 12.8 - - + -
40s PHE 2.9 18.3 + - - +
41s ILE* 3.8 7.9 - - - +
42s GLN 3.2 0.2 - - - -
43s LEU* 1.3 78.6 - - - +
45s LEU* 1.3 60.7 + - - +
47s ALA* 3.4 12.0 + - - +
49s TYR* 6.1 1.1 - - - -
164s CYS* 3.6 38.6 - - + +
165s GLU 5.4 2.2 - - - +
166s VAL* 5.8 4.3 - - + -
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Residues in contact with LEU 45 (chain s).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41s ILE 2.9 19.4 + - - +
42s GLN* 3.2 6.2 + - - +
44s CYS* 1.3 71.5 - - - +
46s GLU* 1.3 60.8 + - - +
47s ALA* 3.1 6.4 + - - +
174s ILE 6.3 0.7 - - - -
175s ILE* 4.7 13.0 - - + +
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Residues in contact with GLU 46 (chain s).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42s GLN 2.9 17.4 + - - +
43s LEU* 4.2 3.1 - - - +
44s CYS 3.3 0.6 - - - -
45s LEU* 1.3 75.4 - - - +
47s ALA* 1.3 66.9 + - - +
48s TYR* 3.5 14.6 + - + +
175s ILE* 4.6 24.4 - - + +
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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