Contacts of the helix formed by residues 28 - 41 (chain A) in PDB entry 5A91
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 SER 28 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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29A VAL* 1.3 63.7 + - - +
30A GLN* 3.2 5.6 - - - +
31A GLN* 3.1 21.0 + - - +
32A GLN* 2.8 45.2 + - - +
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Residues in contact with VAL 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 SER* 1.3 77.6 - - - +
30A GLN* 1.3 64.3 + - + +
32A GLN* 3.1 17.8 + - - +
33A LEU* 2.9 24.9 + - + +
57A ILE* 3.7 40.2 - - + -
285A ILE* 4.0 23.8 - - + +
286A VAL* 4.1 8.1 - - + -
288A HIS* 6.4 0.2 - - + -
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Residues in contact with GLN 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 SER 3.2 2.8 - - - +
29A VAL* 1.3 77.3 - - + +
31A GLN* 1.3 70.0 + - - +
33A LEU* 3.2 6.7 + - - +
34A GLU* 2.9 35.7 + - - +
57A ILE* 4.1 14.1 - - - +
59A LEU 2.8 37.9 + - - +
60A TYR* 3.6 18.8 - - - -
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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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28A SER* 3.1 22.0 + - - +
30A GLN* 1.3 82.2 - - - +
32A GLN* 1.3 57.7 + - + +
34A GLU* 3.4 18.5 + - - +
35A ALA* 3.0 28.9 + - - +
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Residues in contact with GLN 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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28A SER* 2.8 29.0 + - - +
29A VAL* 3.5 27.1 + - - +
31A GLN* 1.3 74.8 - - + +
33A LEU* 1.3 59.0 + - - +
35A ALA* 3.4 6.3 + - - +
36A LEU* 3.0 27.4 + - - +
285A ILE* 3.8 35.6 - - + +
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Residues in contact with LEU 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 VAL* 2.9 25.0 + - + +
30A GLN* 3.8 8.1 - - - +
32A GLN* 1.3 74.1 - - - +
34A GLU* 1.3 65.6 + - - +
36A LEU* 3.2 4.7 + - + +
37A GLU* 2.9 24.3 + - - +
44A LEU* 4.0 16.9 - - + +
46A VAL* 4.4 6.7 - - + -
57A ILE* 4.3 9.2 - - + -
60A TYR* 3.8 37.5 - - + -
282A ALA* 4.3 14.8 - - + -
285A ILE* 3.8 28.3 - - + -
286A VAL* 3.9 24.0 - - + -
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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 GLN* 2.9 27.9 + - - +
31A GLN* 3.6 23.0 - - + +
32A GLN 3.3 0.2 - - - -
33A LEU* 1.3 76.2 - - - +
35A ALA* 1.3 57.3 + - - +
37A GLU* 3.3 3.6 + - - +
38A LYS* 2.9 28.8 + - - +
60A TYR* 3.5 29.7 + - + +
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Residues in contact with ALA 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 3.0 16.9 + - - +
32A GLN* 3.7 6.7 - - - +
33A LEU 3.2 0.2 - - - -
34A GLU* 1.3 78.4 - - - +
36A LEU* 1.3 62.3 + - - +
38A LYS* 3.0 18.1 + - - +
39A SER* 3.2 15.2 + - - -
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Residues in contact with LEU 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 GLN 3.0 17.8 + - - +
33A LEU* 3.2 5.6 + - + +
35A ALA* 1.3 77.0 - - - +
37A GLU* 1.3 59.4 + - - +
39A SER* 2.8 22.5 + - - +
40A SER* 3.2 13.0 + - - -
44A LEU* 3.9 15.0 - - + -
278A ILE* 3.8 30.5 - - + +
281A ALA* 3.9 17.3 - - + -
282A ALA* 3.7 39.0 - - + +
285A ILE* 4.1 11.9 - - + -
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Residues in contact with GLU 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 LEU 2.9 13.7 + - - +
34A GLU 3.6 7.0 - - - +
36A LEU* 1.3 78.2 - - - +
38A LYS* 1.3 64.8 + - - +
40A SER* 2.7 24.5 + - - +
41A GLY 4.0 1.7 + - - -
42A GLY 3.4 19.4 + - - +
43A ARG* 3.4 4.3 - - - +
44A LEU* 2.8 35.8 + - + +
60A TYR* 2.7 26.0 + - + +
61A ARG* 2.8 39.8 + - - -
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Residues in contact with LYS 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 2.9 13.8 + - - +
35A ALA* 3.0 14.8 + - - +
37A GLU* 1.3 76.7 - - - +
39A SER* 1.3 58.9 + - - +
40A SER 3.7 0.2 + - - -
41A GLY* 4.6 2.9 + - - -
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Residues in contact with SER 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 ALA 3.2 9.3 + - - -
36A LEU* 2.8 23.6 + - - +
38A LYS* 1.3 74.7 - - - +
40A SER* 1.3 62.7 + - - +
41A GLY* 3.3 3.6 + - - -
275A ARG* 5.6 0.2 + - - -
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Residues in contact with SER 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 LEU 3.2 15.4 + - - -
37A GLU* 2.7 20.5 + - - -
39A SER* 1.3 79.5 - - - +
41A GLY* 1.3 58.5 + - - +
42A GLY 3.0 14.9 + - - -
265A PHE* 3.3 28.8 - - - -
267A GLN* 4.7 2.9 - - - +
275A ARG* 3.3 23.5 + - - +
278A ILE* 3.9 20.6 - - - -
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Residues in contact with GLY 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 GLU 4.0 2.6 + - - -
38A LYS 4.6 2.8 + - - -
39A SER 3.3 4.6 + - - -
40A SER* 1.3 78.7 + - - +
42A GLY* 1.3 56.0 + - - +
267A GLN* 3.8 10.4 - - - +
268A PRO* 3.3 23.1 - - - +
269A GLU* 4.8 1.2 - - - +
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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