Contacts of the helix formed by residues 57 - 66 (chain D) in PDB entry 2AXZ
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 ASN 57 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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108C GLN* 5.5 1.1 - - - -
151C ILE* 5.5 4.7 - - - +
185C ASP* 4.4 25.2 + - + +
55D GLY 4.0 1.4 + - - -
56D VAL* 1.3 73.5 - - - +
58D PHE* 1.3 61.3 + - - +
59D PHE* 2.5 43.2 + - - +
60D GLU* 3.0 28.2 + - + +
61D ILE* 3.0 28.8 + - - +
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Residues in contact with PHE 58 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62C LEU* 3.8 18.6 - - + -
67C MSE 4.3 14.6 - - - -
44D VAL* 4.2 21.1 - - + -
47D LEU* 3.8 29.3 - - + +
48D SER* 3.8 32.1 - - - -
51D SER* 3.1 22.4 + - - +
57D ASN* 1.3 77.6 + - - +
59D PHE* 1.3 85.7 + + + +
61D ILE* 3.3 7.6 + - - +
62D LEU* 3.3 47.5 + - + +
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Residues in contact with PHE 59 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59C PHE* 3.2 37.0 - + + -
62C LEU* 4.1 18.6 - - + -
63C ASN* 3.7 18.2 - - - -
67C MSE 3.4 43.5 - - + -
182C PHE 5.3 0.2 - - - -
185C ASP* 5.0 12.3 - - - +
57D ASN* 2.5 21.0 + - - +
58D PHE* 1.3 85.9 - + + +
60D GLU* 1.3 58.4 + - - +
62D LEU* 3.3 6.6 + - - +
63D ASN* 2.9 32.9 + - - +
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Residues in contact with GLU 60 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149C PHE* 3.2 14.7 - - - +
150C GLY* 2.9 27.8 + - - -
151C ILE 4.2 1.9 + - - -
182C PHE* 3.6 28.9 - - + +
183C GLY* 5.8 0.2 - - - -
185C ASP* 6.5 0.2 - - + -
186C TYR* 4.1 8.4 + - + +
56D VAL* 3.9 8.3 - - + +
57D ASN* 3.0 31.5 + - + +
59D PHE* 1.3 74.7 - - - +
61D ILE* 1.3 60.3 + - - +
63D ASN* 3.1 2.8 + - - +
64D ARG* 2.8 69.8 + - - +
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Residues in contact with ILE 61 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4D ILE* 4.8 7.4 - - + -
7D VAL* 4.0 19.9 - - + +
8D LEU* 4.7 7.2 - - + -
11D ILE* 5.4 3.8 - - + -
47D LEU* 4.1 24.9 - - + -
51D SER* 3.7 33.7 - - - +
54D LEU* 4.1 18.8 - - + -
56D VAL* 3.9 17.3 - - + +
57D ASN 3.0 17.3 + - - +
58D PHE* 3.4 7.0 - - - +
60D GLU* 1.3 77.7 - - - +
62D LEU* 1.3 63.1 + - - +
64D ARG* 3.3 9.9 + - - +
65D ALA* 3.0 21.1 + - - +
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Residues in contact with LEU 62 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44C VAL* 4.0 8.1 - - + -
58C PHE* 3.8 24.5 - - + -
59C PHE* 4.0 9.2 - - + -
62C LEU* 3.9 4.3 - - + -
4D ILE* 3.9 10.5 - - + -
47D LEU* 3.7 24.5 - - + -
58D PHE* 3.3 39.7 + - + +
59D PHE* 3.6 8.1 - - - +
60D GLU 3.2 0.4 - - - -
61D ILE* 1.3 78.4 - - - +
63D ASN* 1.3 64.3 + - - +
65D ALA* 3.1 10.9 + - - +
66D GLY 3.2 0.5 + - - -
67D MSE 2.9 56.3 + - + +
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Residues in contact with ASN 63 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59C PHE* 3.8 18.2 - - - -
182C PHE* 3.7 21.4 - - - +
183C GLY* 3.0 29.1 - - - +
59D PHE* 2.9 21.3 + - - +
60D GLU 3.1 8.5 + - - +
62D LEU* 1.3 76.3 - - - +
64D ARG* 1.3 63.5 + - - +
66D GLY* 2.9 15.9 + - - -
67D MSE 3.6 1.1 + - - -
68D ASN* 3.2 47.6 + - - +
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Residues in contact with ARG 64 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147C THR* 5.0 6.0 - - - +
148C PHE 3.4 14.6 + - - -
149C PHE* 3.4 27.3 - - - +
182C PHE* 3.3 61.4 - - + -
186C TYR* 3.9 4.2 - - - -
7D VAL* 3.8 18.0 - - + +
10D GLN* 4.8 10.9 - - - +
11D ILE* 4.3 21.5 - - - -
56D VAL* 5.1 2.1 - - - +
60D GLU* 2.8 49.4 + - - +
61D ILE* 3.6 7.2 - - - +
63D ASN* 1.3 75.8 - - - +
65D ALA* 1.3 60.8 + - - +
66D GLY* 3.4 1.0 + - - -
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Residues in contact with ALA 65 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2D PHE* 3.7 22.0 - - + +
3D LYS* 4.2 5.0 + - - +
4D ILE* 3.8 40.2 - - + +
7D VAL* 3.6 12.1 - - + +
61D ILE 3.0 12.9 + - - +
62D LEU* 3.3 13.0 - - - +
63D ASN 3.1 0.4 - - - -
64D ARG* 1.3 78.4 - - - +
66D GLY* 1.3 55.4 + - - +
67D MSE 4.9 1.3 - - + -
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Residues in contact with GLY 66 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2D PHE* 3.9 14.5 - - - -
63D ASN 2.9 8.8 + - - -
64D ARG 3.2 1.7 - - - -
65D ALA* 1.3 79.7 - - - +
67D MSE 1.3 58.8 + - - +
68D ASN* 2.8 15.8 + - - +
72D VAL* 3.3 26.4 - - - +
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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