Contacts of the helix formed by residues 38 - 49 (chain A) in PDB entry 6AF6
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 38 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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31A ARG* 3.8 24.5 - - - +
36A ILE* 3.8 10.1 + - - -
37A LEU* 1.3 72.1 - - - +
39A THR* 1.3 59.5 + - - +
40A GLU* 3.7 6.9 + - - +
41A LEU* 3.2 30.1 + - - +
42A TRP* 2.8 27.4 + - - +
82A ASP* 5.8 0.4 + - - -
85A LEU* 4.2 5.3 - - - +
502A O4B 5.4 2.6 - - - -
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Residues in contact with THR 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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37A LEU* 3.3 21.9 + - + +
38A SER* 1.3 73.2 - - - +
40A GLU* 1.3 62.9 + - - +
42A TRP* 3.5 6.4 - - - +
43A LYS* 2.9 47.0 + - - +
122A ILE* 4.2 19.1 - - + -
164A ILE* 4.4 17.0 - - + -
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Residues in contact with GLU 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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38A SER* 3.2 5.3 + - - +
39A THR* 1.3 81.9 + - - +
41A LEU* 1.3 61.3 + - - +
43A LYS* 3.3 9.9 + - + +
44A LYS* 3.1 27.1 + - - +
502A O4B 3.8 41.5 - - - +
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Residues in contact with LEU 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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23A VAL* 4.1 15.7 - - + +
24A LEU* 3.7 27.2 - - + +
31A ARG* 3.3 46.4 - - - +
38A SER* 3.2 19.4 + - - +
40A GLU* 1.3 75.0 - - - +
42A TRP* 1.3 67.2 + - - +
44A LYS* 3.2 6.1 + - + +
45A ALA* 3.0 24.3 + - - +
85A LEU* 4.2 7.4 - - + -
502A O4B 3.7 36.5 - - - -
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Residues in contact with TRP 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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37A LEU* 4.0 9.6 - - + -
38A SER 2.8 18.4 + - - +
39A THR* 3.5 9.9 - - - +
41A LEU* 1.3 76.0 - - - +
43A LYS* 1.3 68.5 + - + +
45A ALA* 3.3 6.9 + - - +
46A ALA* 2.8 29.7 + - + -
85A LEU* 3.4 28.2 - - + +
88A SER* 2.8 27.9 + - - -
89A LEU* 3.6 24.3 - - + +
92A HIS* 3.5 55.2 - + + -
119A GLY* 3.8 23.8 - - - -
122A ILE* 3.6 38.1 - - + -
161A ASN* 4.8 0.4 + - - -
164A ILE* 5.0 0.8 - - + +
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Residues in contact with LYS 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 THR* 2.9 29.4 + - - +
40A GLU* 3.8 8.3 - - + +
42A TRP* 1.3 86.9 - - + +
44A LYS* 1.3 56.6 + - + +
46A ALA* 3.3 4.3 + - - +
47A ALA* 2.9 31.4 + - - +
118A THR 4.0 3.0 - - - +
119A GLY 2.9 32.7 + - - +
120A LYS* 3.0 21.9 + - - +
122A ILE* 4.4 19.9 - - - +
166A ASP* 4.8 2.8 + - - -
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Residues in contact with LYS 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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19A PHE* 3.8 14.7 - - + -
23A VAL* 5.0 2.5 - - + -
40A GLU 3.1 15.9 + - - +
41A LEU* 3.2 11.2 + - + +
43A LYS* 1.3 76.3 - - + +
45A ALA* 1.3 58.7 + - - +
47A ALA* 3.4 4.8 + - - +
48A TYR* 2.8 30.0 + - - +
502A O4B 2.7 117.9 + - - +
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Residues in contact with ALA 45 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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19A PHE* 3.7 23.5 - - + -
24A LEU* 4.0 9.9 - - + -
41A LEU 3.0 15.5 + - - +
42A TRP* 3.6 2.2 - - - +
44A LYS* 1.3 74.1 - - - +
46A ALA* 1.3 66.3 + - - +
48A TYR* 3.3 6.4 + - - +
49A GLY 3.3 0.9 + - - -
50A PHE* 3.2 31.1 + - + -
89A LEU* 3.5 27.8 - - + -
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Residues in contact with ALA 46 (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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42A TRP* 2.8 27.6 + - + +
43A LYS 3.3 4.5 + - - +
45A ALA* 1.3 76.0 - - - +
47A ALA* 1.3 61.8 + - - +
49A GLY 3.1 10.6 + - - -
51A ALA* 3.4 34.7 + - + +
52A HIS* 3.4 12.6 + - - -
89A LEU* 3.9 6.8 - - + +
117A VAL 3.6 2.6 - - - +
119A GLY* 3.7 22.7 - - - +
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Residues in contact with ALA 47 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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43A LYS 2.9 17.3 + - - +
44A LYS* 3.9 5.2 - - - +
46A ALA* 1.3 75.2 - - - +
48A TYR* 1.3 65.6 + - - +
49A GLY 3.3 0.7 + - - -
52A HIS* 3.6 16.6 - - - -
118A THR* 3.6 22.2 + - - +
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Residues in contact with TYR 48 (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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12A ILE 4.5 1.4 + - - -
15A SER* 2.4 51.0 + - - -
16A ALA* 3.0 4.6 + - - +
19A PHE* 3.6 37.5 - + + -
44A LYS 2.8 19.5 + - - +
45A ALA 3.3 4.4 + - - +
47A ALA* 1.3 76.0 - - - +
49A GLY* 1.3 59.9 + - - +
50A PHE* 3.5 27.8 - + - -
52A HIS* 4.4 1.8 - - - -
72A MET* 3.6 24.7 - - + +
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Residues in contact with GLY 49 (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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46A ALA 3.1 4.0 + - - -
48A TYR* 1.3 81.9 - - - +
50A PHE* 1.3 66.8 + - - +
51A ALA 3.2 2.9 - - - -
52A HIS* 3.1 40.0 + - - +
53A GLY 4.1 3.1 + - - -
64A LEU* 5.7 0.3 - - - +
72A MET* 3.9 19.6 - - - +
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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