Contacts of the helix formed by residues 32 - 44 (chain A) in PDB entry 6A08
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 GLU 32 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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27A GLY* 3.4 0.5 - - - -
28A GLY 2.9 40.6 + - - +
29A SER 2.9 14.7 + - - +
30A GLY 4.2 4.7 - - - +
31A THR* 1.3 80.7 - - - +
33A ALA* 1.3 64.8 + - - +
34A SER 3.3 2.5 - - - +
35A LEU* 3.4 18.8 + - + +
36A VAL* 3.1 29.4 + - + +
165A ARG* 2.9 48.7 + - - +
254A GLY 5.2 0.4 - - - -
258A ASP* 3.8 0.4 - - - -
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Residues in contact with ALA 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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31A THR* 3.2 14.7 - - - +
32A GLU* 1.3 78.8 - - - +
34A SER* 1.3 57.1 + - - +
36A VAL* 3.6 4.6 + - - +
37A ALA* 2.9 29.3 + - - +
258A ASP* 2.9 12.8 + - - +
259A GLY* 4.7 9.6 - - - +
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Residues in contact with SER 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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32A GLU* 3.3 0.4 - - - +
33A ALA* 1.3 74.7 - - - +
35A LEU* 1.3 65.3 + - - +
37A ALA* 3.8 6.3 - - - +
38A ASN* 3.1 30.0 + - - +
251A ASN* 3.6 10.8 + - - +
254A GLY* 3.9 14.8 - - - -
257A LEU 4.0 7.2 - - - -
258A ASP* 3.5 5.2 + - - -
259A GLY* 2.8 27.0 + - - -
260A ALA 2.7 28.5 + - - -
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Residues in contact with LEU 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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26A ALA 3.5 18.8 - - - +
28A GLY* 4.0 5.2 - - - +
32A GLU* 3.4 41.8 + - + +
34A SER* 1.3 81.6 - - - +
36A VAL* 1.3 67.3 + - + +
38A ASN* 3.3 17.7 + - + +
39A ARG* 3.9 7.1 + - - +
165A ARG* 4.5 3.8 - - - +
253A GLY 3.4 22.2 - - - +
254A GLY* 3.8 12.8 + - - +
287A ARG* 5.9 1.6 - - - +
307A ARG* 3.5 24.0 - - - +
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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 GLU* 3.1 20.4 + - + +
33A ALA* 4.0 3.8 - - - +
35A LEU* 1.3 81.2 - - + +
37A ALA* 1.3 64.0 + - - +
39A ARG* 3.0 11.5 + - + +
40A THR* 3.0 28.5 + - - +
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Residues in contact with ALA 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 ALA 2.9 19.4 + - - +
34A SER* 3.8 6.7 - - - +
35A LEU 3.3 0.4 - - - -
36A VAL* 1.3 76.4 - - - +
38A ASN* 1.3 63.7 + - - +
40A THR* 3.9 9.6 - - - -
41A ALA* 2.9 28.2 + - - +
260A ALA 5.6 0.2 - - - +
262A PRO* 3.6 22.9 - - + -
265A GLU* 5.6 1.6 - - - +
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Residues in contact with ASN 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 SER 3.1 12.2 + - - -
35A LEU* 3.6 10.3 + - + +
36A VAL 3.2 0.4 - - - -
37A ALA* 1.3 76.0 - - - +
39A ARG* 1.3 63.7 + - + +
41A ALA* 4.1 1.7 - - - +
42A LEU* 3.5 25.6 + - - +
251A ASN* 3.0 39.7 + - - +
253A GLY* 3.8 21.2 - - - -
262A PRO* 3.3 18.2 - - - +
263A GLY 4.5 1.4 + - - -
264A ILE* 4.7 2.4 - - - +
283A ASP 5.4 0.7 - - - -
284A GLY* 3.8 32.9 - - - +
285A GLY* 4.3 3.1 - - - +
402A FMN 5.3 0.4 + - - -
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Residues in contact with ARG 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 LEU 4.7 6.1 - - - +
36A VAL* 3.0 10.7 + - + +
38A ASN* 1.3 77.1 - - + +
40A THR* 1.3 66.1 + - - +
42A LEU* 3.2 9.5 + - - +
43A GLU* 3.0 64.1 + - - +
285A GLY* 2.7 45.3 + - - -
287A ARG* 3.6 22.9 - - - +
291A ASP* 2.8 27.9 + - - -
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Residues in contact with THR 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* 3.0 27.8 + - - +
37A ALA* 3.9 9.1 - - - -
39A ARG* 1.3 76.0 - - - +
41A ALA* 1.3 63.9 + - - +
43A GLU* 3.1 12.5 + - - +
44A ARG* 3.1 37.0 + - + +
357A VAL* 6.4 1.8 - - - -
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Residues in contact with ALA 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 ALA 2.9 18.5 + - - +
38A ASN 4.1 0.7 - - - +
40A THR* 1.3 78.4 - - - +
42A LEU* 1.3 61.4 + - - +
44A ARG* 3.3 22.3 + - - +
45A VAL* 3.4 15.9 - - - +
262A PRO* 4.1 2.9 - - + -
264A ILE* 3.3 27.3 - - + +
265A GLU* 3.6 28.7 - - + +
354A LEU* 5.5 0.2 - - - +
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Residues in contact with LEU 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 ASN 3.5 9.0 + - - +
39A ARG* 3.2 20.2 + - - +
41A ALA* 1.3 79.1 - - - +
43A GLU* 1.3 61.5 + - + +
45A VAL* 3.1 15.5 + - + +
264A ILE* 4.0 31.9 - - + -
284A GLY 3.9 9.2 - - - +
285A GLY 3.2 34.8 - - - +
286A ILE* 4.0 12.1 - - + -
291A ASP* 4.1 18.8 - - - +
294A LYS* 3.0 46.7 + - + +
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Residues in contact with GLU 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 ARG* 3.0 53.8 + - - +
40A THR* 3.1 11.3 + - + +
42A LEU* 1.3 77.1 - - - +
44A ARG* 1.3 59.6 + - - +
45A VAL 3.3 2.0 + - - +
46A PHE* 3.7 13.7 - - - -
294A LYS* 4.2 7.8 + - - +
357A VAL* 3.5 27.5 - - - +
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Residues in contact with ARG 44 (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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40A THR* 3.1 26.6 + - + +
41A ALA* 3.6 16.6 + - - +
42A LEU 3.1 0.6 - - - -
43A GLU* 1.3 75.6 - - - +
45A VAL* 1.3 61.4 + - - +
46A PHE* 3.5 3.3 - - - -
265A GLU* 3.8 29.7 + - - +
354A LEU* 3.4 32.7 - - + +
355A GLY 2.8 46.2 + - - +
356A VAL* 5.4 1.6 - - - +
357A VAL* 4.4 16.4 - - - +
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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