Contacts of the helix formed by residues 55 - 67 (chain A) in PDB entry 1O69
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 55 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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53A LEU* 3.3 3.8 - - - +
54A ASN* 1.3 85.7 + - - +
56A ALA* 1.3 63.8 + - - +
57A THR* 3.4 4.5 + - - -
58A ALA* 2.8 33.5 + - - +
59A ALA* 3.2 16.1 + - - +
191A GLY 3.7 5.6 - - - +
192A GLY* 3.6 11.8 - - - -
402A X04 3.4 17.3 - - - -
54B ASN* 5.6 0.4 - - - -
227B ASN* 3.6 26.1 + - - +
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Residues in contact with ALA 56 (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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55A SER* 1.3 70.9 - - - +
57A THR* 1.3 65.5 + - - +
59A ALA* 3.1 4.4 + - - +
60A LEU* 2.9 23.2 + - - +
157A ALA* 4.3 2.7 - - + -
177A VAL* 3.4 27.4 - - + +
178A TYR 3.9 2.7 - - - +
179A SER* 3.6 16.4 - - - -
192A GLY* 3.8 5.1 - - - -
402A X04 2.8 39.7 + - - +
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Residues in contact with THR 57 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A SER* 3.2 4.9 - - - -
56A ALA* 1.3 79.0 - - - +
58A ALA* 1.3 62.5 + - - +
60A LEU* 3.3 2.8 + - - -
61A HIS* 3.0 22.6 + - - +
84A ALA* 3.5 27.3 + - - +
88A PRO* 3.7 11.8 - - + +
91A TYR* 3.6 28.0 - - + +
402A X04 2.7 23.2 + - - -
211B GLN* 3.2 23.2 + - - +
227B ASN* 4.2 7.4 - - - +
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Residues in contact with ALA 58 (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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53A LEU* 4.2 5.6 - - + -
54A ASN* 3.9 7.2 - - - +
55A SER* 2.8 25.6 + - - +
57A THR* 1.3 76.2 - - - +
59A ALA* 1.3 56.4 + - - +
61A HIS* 3.4 3.7 + - - +
62A LEU* 3.0 32.7 + - - +
228A TYR* 3.7 48.6 - - + -
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Residues in contact with ALA 59 (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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53A LEU* 3.4 24.6 - - + +
55A SER 3.2 10.6 + - - +
56A ALA* 3.1 9.5 + - - +
58A ALA* 1.3 76.3 - - - +
60A LEU* 1.3 57.0 + - - +
62A LEU* 3.3 3.0 + - - +
63A ALA* 2.8 30.1 + - - +
177A VAL* 3.6 25.8 - - + -
193A MET 4.1 6.7 - - - +
194A LEU* 3.7 14.9 - - + +
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Residues in contact with LEU 60 (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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56A ALA 2.9 15.1 + - - +
57A THR* 3.8 5.4 - - - +
59A ALA* 1.3 74.2 - - - +
61A HIS* 1.3 59.1 + - - +
63A ALA* 3.2 4.8 + - - +
64A LEU* 2.9 34.3 + - - +
84A ALA 4.1 3.8 - - - +
85A SER* 3.7 24.5 - - - +
88A PRO* 4.0 12.3 - - + -
127A ILE* 4.1 18.4 - - + -
153A ILE* 3.6 29.4 - - + -
155A ASP* 4.3 16.6 - - + +
177A VAL* 3.7 17.0 - - + -
402A X04 3.6 26.7 - - - +
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Residues in contact with HIS 61 (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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57A THR 3.0 12.8 + - - +
58A ALA 3.4 9.9 - - - +
59A ALA 3.4 0.2 - - - -
60A LEU* 1.3 74.9 - - - +
62A LEU* 1.3 65.0 + - - +
64A LEU* 3.4 2.8 + - - +
65A ARG* 3.0 20.3 + - + +
88A PRO* 3.7 14.2 - - + +
91A TYR* 3.6 32.0 - + + +
92A LEU* 3.8 29.3 - - + +
226A TYR* 3.5 36.6 + + - -
228A TYR* 2.6 30.3 + + + +
91B TYR* 6.0 1.8 - + - -
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Residues in contact with LEU 62 (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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53A LEU* 3.8 33.4 - - + -
58A ALA 3.0 16.9 + - - +
59A ALA 3.7 3.8 - - - +
61A HIS* 1.3 77.5 - - - +
63A ALA* 1.3 54.4 + - - +
65A ARG* 3.2 4.5 + - + +
66A VAL* 2.8 41.3 + - + +
194A LEU* 4.3 3.6 - - + -
205A ALA* 3.6 35.0 - - + +
208A TYR* 3.8 16.4 - - + -
209A SER* 4.0 3.8 - - - -
226A TYR* 3.7 37.0 - - + -
228A TYR* 3.8 14.4 - - + -
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Residues in contact with ALA 63 (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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59A ALA 2.8 20.5 + - - +
60A LEU* 3.5 7.4 - - - +
62A LEU* 1.3 72.8 - - - +
64A LEU* 1.3 56.4 + - - +
66A VAL* 3.6 9.3 - - - +
67A ALA* 2.9 32.6 + - - +
153A ILE* 4.1 18.6 - - + -
175A PHE* 3.9 24.3 - - + -
177A VAL* 5.1 0.2 - - + -
194A LEU* 3.9 18.5 - - + +
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Residues in contact with LEU 64 (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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60A LEU 2.9 18.3 + - - +
61A HIS 3.8 1.8 - - - +
63A ALA* 1.3 73.1 - - - +
65A ARG* 1.3 63.6 + - - +
67A ALA* 3.4 2.6 + - - +
68A GLY 3.3 4.2 + - - -
69A VAL* 3.1 42.1 + - + +
75A VAL* 4.1 15.9 - - + -
88A PRO* 3.6 44.4 - - + +
89A ILE* 3.7 9.6 - - + +
92A LEU* 3.6 16.4 - - + -
125A ALA* 4.4 0.7 - - + -
127A ILE* 3.9 24.0 - - + -
153A ILE* 3.5 24.5 - - + -
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Residues in contact with ARG 65 (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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61A HIS* 3.0 17.1 + - + +
62A LEU* 3.8 7.2 - - + +
64A LEU* 1.3 77.5 - - - +
66A VAL* 1.3 59.2 + - + +
68A GLY* 3.0 20.1 + - - -
69A VAL 4.1 5.2 + - - +
70A LYS* 4.9 8.4 + - - +
92A LEU* 3.8 21.0 - - + +
208A TYR* 3.4 29.3 + - + +
223A ASP* 2.8 39.8 + - - -
224A TYR* 3.0 40.5 + - - -
226A TYR* 2.9 36.9 + - - +
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Residues in contact with VAL 66 (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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62A LEU 2.8 26.9 + - - +
63A ALA* 3.6 3.1 - - - +
65A ARG* 1.3 72.6 - - - +
67A ALA* 1.3 60.8 + - - +
68A GLY* 3.1 1.8 + - - -
175A PHE* 3.3 35.4 - - + -
201A LYS* 4.0 26.1 - - + +
204A LYS* 4.0 11.2 - - + -
205A ALA* 3.8 30.5 - - + +
208A TYR* 3.9 25.6 - - + -
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Residues in contact with ALA 67 (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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63A ALA 2.9 20.7 + - - +
64A LEU* 3.6 8.1 - - - +
65A ARG 3.2 0.2 - - - -
66A VAL* 1.3 77.5 - - - +
68A GLY* 1.3 50.1 + - - +
69A VAL* 3.5 6.3 - - + -
124A LYS* 2.7 29.0 + - - +
125A ALA* 5.4 0.9 - - + -
151A VAL* 4.2 33.3 - - + +
153A ILE* 4.7 4.7 - - + -
175A PHE* 4.2 8.7 - - + -
201A LYS* 5.5 4.9 - - - +
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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