Contacts of the helix formed by residues 72 - 82 (chain U) in PDB entry 2AXT
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 TYR 72 (chain U).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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320C ARG* 5.4 1.7 + - - -
324C LEU* 3.7 38.3 - - + +
62U ILE* 3.9 26.1 - - + +
63U ALA* 4.4 3.6 - - - -
65U PHE 3.7 11.4 + - - +
66U ILE* 3.1 52.1 - - + +
68U TYR 4.7 0.6 + - - -
71U LEU* 1.3 86.7 - - - +
73U PRO* 1.3 103.3 - - + +
74U THR 2.9 2.5 + - - -
76U ALA* 3.0 19.6 + - + +
75V ASN* 5.0 7.1 + - - -
77V SER* 4.6 9.7 + - - -
78V LEU* 4.5 13.7 - - + -
107V THR* 5.6 2.7 - - + -
108V TYR* 4.4 14.3 - - + -
552V HEM 5.8 1.6 - - - -
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Residues in contact with PRO 73 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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324C LEU* 4.6 9.4 - - + +
72U TYR* 1.3 121.7 - - + +
74U THR* 1.3 63.3 + - - +
76U ALA* 4.4 1.0 - - - +
77U LYS* 3.8 17.5 + - - +
107V THR* 3.2 29.8 - - + -
108V TYR* 3.6 7.6 - - + +
109V ASP* 3.0 44.4 - - + +
112V GLN* 5.7 2.5 - - - +
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Residues in contact with THR 74 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72U TYR 2.9 2.0 + - - -
73U PRO* 1.3 80.3 - - - +
75U LEU* 1.3 65.2 + - - +
77U LYS* 3.7 7.5 + - - +
78U LEU* 3.4 23.0 + - + +
101U GLN* 4.0 21.5 - - - +
109V ASP* 2.9 17.8 + - - -
111V GLU* 3.5 30.5 + - - +
112V GLN* 4.9 7.4 + - - +
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Residues in contact with LEU 75 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70U GLY 4.4 10.8 - - - +
71U LEU* 3.2 36.2 + - + +
72U TYR 3.2 1.6 + - - -
74U THR* 1.3 77.6 - - - +
76U ALA* 1.3 54.9 + - - +
78U LEU* 2.7 44.1 + - + +
79U ILE* 2.7 28.1 + - + +
94U ILE* 6.4 0.2 - - + -
97U LEU* 4.3 1.8 - - + -
101U GLN* 4.0 36.6 - - + +
104U ILE* 4.5 11.4 - - + -
105U LEU* 4.1 28.7 - - + -
109V ASP* 4.8 0.6 + - - -
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Residues in contact with ALA 76 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62U ILE* 3.7 15.9 - - + -
65U PHE* 3.2 43.5 - - + -
71U LEU 3.2 1.6 + - - -
72U TYR* 3.0 23.8 + - + +
73U PRO 4.4 0.4 - - - +
75U LEU* 1.3 77.0 - - - +
77U LYS* 1.3 62.4 + - - +
79U ILE* 4.3 3.1 - - - -
80U VAL* 3.0 31.4 + - - +
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Residues in contact with LYS 77 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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322C GLN 4.4 4.2 + - - -
323C LYS* 4.7 4.4 - - - +
324C LEU* 3.7 35.9 - - + +
325C GLY* 3.7 20.1 - - - +
62U ILE* 4.0 11.8 - - + +
73U PRO 3.8 13.0 + - - +
74U THR* 3.7 10.3 + - - +
75U LEU 3.1 0.2 - - - -
76U ALA* 1.3 79.6 - - - +
78U LEU* 1.3 58.5 + - + +
80U VAL* 4.3 1.2 - - - +
81U LYS* 2.8 42.8 + - + +
128U TYR* 5.4 0.7 + - - -
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Residues in contact with LEU 78 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74U THR* 3.4 13.4 + - + +
75U LEU* 2.7 28.4 + - + +
77U LYS* 1.3 72.5 - - + +
79U ILE* 1.3 69.2 + - - +
81U LYS* 3.0 11.2 + - + -
82U ASN* 2.7 36.0 + - - +
94U ILE* 4.2 11.7 - - + -
95U PRO 5.2 4.0 - - - +
96U GLY 5.7 0.9 - - - +
97U LEU* 3.4 32.1 - - + -
101U GLN* 4.0 12.1 - - - +
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Residues in contact with ILE 79 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57U LEU* 3.2 35.2 - - + +
65U PHE* 3.7 33.4 - - + -
71U LEU* 5.2 2.5 - - + -
75U LEU* 2.7 32.8 + - + +
76U ALA* 3.8 3.8 - - - +
78U LEU* 1.3 73.9 - - + +
80U VAL* 1.3 64.1 + - - +
82U ASN 3.0 3.3 + - - -
83U ALA 4.5 0.2 - - - +
85U TYR* 2.6 42.7 + - + +
91U VAL* 4.3 13.7 - - + -
94U ILE* 4.1 4.0 - - + +
105U LEU* 4.2 21.1 - - + -
112U PHE* 4.4 4.9 - - + -
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Residues in contact with VAL 80 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62U ILE* 4.0 18.4 - - + +
65U PHE* 3.7 22.2 - - + -
76U ALA 3.0 17.6 + - - +
77U LYS 4.3 1.3 - - - +
79U ILE* 1.3 76.3 - - - +
81U LYS* 1.3 58.1 + - - +
82U ASN 2.9 5.7 + - - -
83U ALA* 4.0 8.0 + - - +
127U ARG* 4.1 49.4 + - + +
128U TYR* 3.6 33.5 + - + +
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Residues in contact with LYS 81 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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325C GLY* 2.7 38.7 + - - +
326C ALA 4.8 1.2 + - - -
327C ASN* 4.1 19.2 + - - +
77U LYS* 2.8 31.6 + - + +
78U LEU* 3.0 7.1 + - + +
80U VAL* 1.3 74.8 - - - +
82U ASN* 1.3 65.1 + - - +
83U ALA 3.7 3.1 + - - -
128U TYR* 3.8 11.4 + - - +
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Residues in contact with ASN 82 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78U LEU* 2.7 29.7 + - - +
79U ILE 3.0 1.2 + - - -
80U VAL 2.9 4.4 + - - -
81U LYS* 1.3 84.9 - - - +
83U ALA* 1.3 72.5 + - - +
84U PRO 3.8 1.6 - - - +
85U TYR* 2.8 31.9 + - + +
94U ILE* 3.3 31.8 - - + +
95U PRO* 4.3 12.5 - - - +
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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