Contacts of the helix formed by residues 33 - 45 (chain A) in PDB entry 2AFB
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 GLY 33 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8A GLU 3.5 17.3 - - - -
10A MSE 4.7 11.0 - - - -
32A GLY* 1.3 73.5 - - - -
34A ALA* 1.3 56.9 + - - -
35A GLU 3.4 2.2 - - - -
36A ALA* 3.0 6.6 + - - +
37A ASN* 2.8 44.1 + - - +
316A ASP* 3.8 1.6 + - - -
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Residues in contact with ALA 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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8A GLU 4.6 0.4 + - - -
33A GLY* 1.3 70.7 - - - +
35A GLU* 1.3 71.4 + - - +
37A ASN* 3.3 0.5 + - - +
38A VAL* 3.2 25.7 + - - +
131A HIS* 5.8 0.7 - - - -
133A SER* 4.1 5.4 - - - +
135A ILE* 3.9 16.8 - - + -
166A ASN* 3.7 22.0 - - - +
280A ASP* 3.4 31.1 - - - +
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Residues in contact with GLU 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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5A THR* 2.8 26.8 + - - +
6A PHE 3.1 33.5 - - - +
7A GLY* 3.5 11.1 - - - -
8A GLU 3.9 6.6 + - - +
34A ALA* 1.3 77.7 + - - +
36A ALA* 1.3 65.0 + - - +
38A VAL* 3.3 9.1 + - - +
39A ALA 3.1 13.2 + - - -
51A PHE* 3.7 1.6 - - + -
131A HIS* 4.3 5.2 - - + -
132A PHE* 4.0 7.4 - - - -
133A SER* 2.8 45.2 + - - +
135A ILE* 5.4 2.9 - - - +
136A THR* 2.7 23.4 + - - -
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Residues in contact with ALA 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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9A ILE* 3.9 26.5 - - + -
33A GLY 3.0 10.3 + - - +
35A GLU* 1.3 76.8 + - - +
37A ASN* 1.3 57.5 + - - +
39A ALA* 3.2 4.7 + - - +
40A ALA* 3.0 27.4 + - - +
51A PHE* 3.4 39.8 - - + -
68A LEU* 4.2 6.7 - - + +
317A PHE* 3.9 7.2 - - + -
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Residues in contact with ASN 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 GLY* 2.8 37.1 + - - +
34A ALA 3.5 4.7 - - - +
36A ALA* 1.3 76.2 - - - +
38A VAL* 1.3 58.3 + - - +
40A ALA* 3.2 3.1 + - - +
41A PHE* 3.0 28.1 + - - +
276A VAL* 5.1 1.6 - - - +
277A GLY* 3.9 6.0 - - - +
280A ASP* 2.9 34.0 + - + -
281A SER* 5.6 0.3 + - - -
316A ASP* 3.4 36.0 + - - +
317A PHE* 3.0 30.8 - - - -
318A VAL 5.5 1.0 + - - -
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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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5A THR* 4.2 4.7 - - + -
34A ALA 3.2 16.6 + - - +
35A GLU 3.6 6.7 - - - +
36A ALA 3.2 0.4 - - - -
37A ASN* 1.3 73.4 - - - +
39A ALA* 1.3 66.7 + - - +
41A PHE* 3.1 6.1 + - - +
42A LEU* 3.0 31.8 + - + +
131A HIS* 3.9 27.6 - - + +
280A ASP* 3.5 27.1 - - + +
283A ALA* 4.1 5.8 - - + -
284A GLY* 4.1 6.1 - - - -
287A ILE* 3.7 29.6 - - + -
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Residues in contact with ALA 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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5A THR* 3.7 27.7 - - + +
35A GLU 3.1 5.6 + - - +
36A ALA 3.5 8.5 - - - +
38A VAL* 1.3 76.6 - - - +
40A ALA* 1.3 58.7 + - - +
42A LEU* 3.4 2.1 + - - +
43A ALA* 2.8 27.4 + - - +
49A ALA* 3.3 19.5 - - + +
50A TYR 4.5 2.7 - - - +
51A PHE* 4.1 8.7 - - + -
73A VAL* 3.7 22.9 - - + -
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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 ALA 3.0 11.4 + - - +
37A ASN 3.7 6.1 - - - +
38A VAL 3.2 0.2 - - - -
39A ALA* 1.3 76.9 - - - +
41A PHE* 1.3 58.2 + - - +
43A ALA* 3.4 2.1 + - - +
44A GLN* 2.9 35.0 + - - +
71A PHE* 4.4 8.3 - - + +
73A VAL* 3.6 13.7 - - + +
317A PHE* 3.5 46.2 - - + -
318A VAL* 4.9 1.1 - - - +
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Residues in contact with PHE 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 ASN 3.0 13.3 + - - +
38A VAL* 3.1 8.7 + - - +
40A ALA* 1.3 72.7 - - - +
42A LEU* 1.3 69.1 + - - +
44A GLN* 3.0 5.2 + - - +
45A MSE 2.9 60.5 + - + +
281A SER* 3.9 17.9 - - - -
284A GLY* 3.3 25.1 - - - -
285A ALA* 3.4 32.5 - - + -
288A TYR* 4.2 2.9 - + + -
302A PHE* 4.4 1.8 - + - -
306A ALA* 3.8 23.1 - - + -
318A VAL* 3.6 36.0 - - + +
320A LEU* 4.9 0.4 - - + -
325A ILE* 4.2 4.0 - - + -
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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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3A VAL* 3.5 30.3 - - + -
5A THR* 5.0 0.7 - - + -
38A VAL* 3.0 34.2 + - + +
39A ALA* 3.8 6.1 - - - +
41A PHE* 1.3 78.2 - - + +
43A ALA* 1.3 60.2 + - - +
45A MSE 3.3 6.1 + - - +
46A GLY 3.3 4.7 + - - -
47A LEU* 3.2 39.6 + - + +
49A ALA* 4.1 11.0 - - + -
284A GLY* 3.4 25.1 - - - +
287A ILE* 3.9 13.2 - - + -
288A TYR* 3.8 24.7 - - + +
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Residues in contact with ALA 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 ALA 2.8 20.4 + - - +
40A ALA 3.7 2.5 - - - +
42A LEU* 1.3 72.7 - - - +
44A GLN* 1.3 58.1 + - - +
46A GLY* 2.9 19.6 + - - -
47A LEU 4.1 10.8 - - - +
49A ALA* 3.8 5.7 - - + +
71A PHE 3.4 21.9 - - - +
72A GLY* 3.5 25.4 - - - +
73A VAL* 3.8 7.2 - - + +
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Residues in contact with GLN 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 ALA 2.9 24.4 + - - +
41A PHE 3.0 5.8 + - - +
43A ALA* 1.3 75.0 - - - +
45A MSE 1.3 68.0 + - + +
46A GLY* 3.5 0.7 + - - -
70A LYS 5.2 0.4 + - - -
71A PHE* 3.4 37.6 + - + +
318A VAL* 3.5 28.0 - - + +
319A VAL* 3.6 8.7 - - - +
320A LEU 3.4 39.1 + - - +
321A SER* 5.1 2.6 - - - -
322A ILE* 5.5 0.7 + - - +
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Residues in contact with MSE 45 (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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-3A HIS 5.1 4.0 - - - +
-1A HIS* 5.3 1.6 - - - -
41A PHE* 2.9 51.1 + - + +
42A LEU* 3.6 8.3 - - - +
43A ALA 3.2 0.4 - - - -
44A GLN* 1.3 86.0 - - + +
46A GLY* 1.3 58.0 + - - +
47A LEU* 4.8 0.6 - - + +
288A TYR* 3.6 35.1 + - + -
302A PHE* 4.2 9.2 - - - -
318A VAL* 4.9 0.2 - - + -
320A LEU* 3.5 31.2 - - + +
321A SER 4.4 3.1 - - - -
322A ILE* 3.8 37.5 - - - +
325A ILE* 3.9 25.1 - - + -
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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