Contacts of the helix formed by residues 79 - 89 (chain D) in PDB entry 1AGQ
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 MET 79 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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56C LEU* 3.9 30.1 - - + -
124C LEU* 4.2 15.9 - - + -
125C ARG 3.5 21.8 + - - +
126C LYS 3.6 2.5 + - - +
127C HIS* 3.6 20.4 - - + -
78D THR* 1.3 70.8 - - - +
80D TYR* 1.3 61.8 + - - +
82D LYS* 3.0 18.2 + - + -
83D ILE* 2.8 51.1 + - + +
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Residues in contact with TYR 80 (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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66C PHE* 3.9 11.0 - + - -
67C ARG 3.5 20.6 - - - -
68C TYR* 3.4 8.4 - - - +
69C CYS* 2.9 34.2 + - - +
104C ARG* 3.9 5.4 - - - -
105C PRO* 3.5 31.0 - - + -
108C PHE* 3.7 10.3 - + + -
126C LYS 3.0 20.3 + - - +
127C HIS* 3.6 23.5 - - - +
128C SER 4.2 0.2 - - - -
129C ALA* 3.9 16.4 - - + -
78D THR* 3.6 6.3 - - - +
79D MET* 1.3 77.2 - - - +
81D ASP* 1.3 68.2 + - - +
83D ILE* 3.2 3.2 + - - +
84D LEU* 2.9 54.8 + - + +
99D GLY 4.6 0.3 + - - -
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Residues in contact with ASP 81 (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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104C ARG* 2.9 43.8 + - - -
75D ALA 5.6 0.2 - - - -
76D ALA* 3.6 22.2 - - + +
77D GLU* 4.0 7.5 + - - +
78D THR* 3.2 25.3 + - - +
80D TYR* 1.3 79.7 - - - +
82D LYS* 1.3 66.8 + - - +
84D LEU* 3.9 6.2 - - - +
85D LYS* 3.1 23.7 + - - +
100D GLN* 5.0 2.1 + - - +
101D ALA* 4.4 11.1 + - - +
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Residues in contact with LYS 82 (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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56C LEU* 5.4 1.8 - - + -
75D ALA* 5.4 1.0 - - - +
76D ALA* 3.1 40.8 + - + +
78D THR 3.1 13.9 + - - +
79D MET* 3.0 29.2 + - + +
81D ASP* 1.3 75.5 - - - +
83D ILE* 1.3 58.1 + - - +
85D LYS* 2.6 41.8 - - + +
86D ASN* 2.9 21.2 + - - +
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Residues in contact with ILE 83 (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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54C LEU* 3.6 46.7 - - + +
56C LEU* 4.9 1.6 - - + -
66C PHE* 3.8 16.4 - - + -
124C LEU* 5.1 0.2 - - + -
127C HIS* 3.6 28.7 - - + +
79D MET* 2.8 44.5 + - + +
80D TYR 3.6 3.8 - - - +
82D LYS* 1.3 73.0 - - - +
84D LEU* 1.3 60.9 + - - +
86D ASN* 3.1 7.3 + - - +
87D LEU* 2.8 51.9 + - + +
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Residues in contact with LEU 84 (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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66C PHE* 3.9 26.5 - - + -
68C TYR* 4.1 9.9 - - + -
104C ARG* 4.5 1.1 - - - +
80D TYR* 2.9 44.2 + - + +
81D ASP* 3.9 6.3 - - - +
82D LYS 3.4 0.2 - - - -
83D ILE* 1.3 75.7 - - - +
85D LYS* 1.3 56.9 + - - +
87D LEU* 3.9 3.2 - - - +
88D SER* 2.8 32.7 + - - -
93D LEU* 4.1 18.0 - - + +
98D VAL* 3.3 19.5 - - + +
99D GLY* 3.3 29.4 - - - +
100D GLN* 3.4 15.5 - - - +
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Residues in contact with LYS 85 (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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74D GLU 3.8 20.0 + - - +
76D ALA* 4.2 5.6 - - + -
81D ASP 3.1 10.5 + - - +
82D LYS* 2.6 64.5 - - + +
84D LEU* 1.3 76.2 - - - +
86D ASN* 1.3 68.1 + - - +
88D SER* 3.7 4.2 - - - -
89D ARG* 2.9 30.0 + - - +
100D GLN* 3.6 17.9 + - - +
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Residues in contact with ASN 86 (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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53C ASP 5.6 0.4 - - - -
54C LEU 2.9 30.1 + - - +
55C GLY* 3.4 20.2 + - - -
56C LEU* 3.6 14.3 - - - +
82D LYS* 2.9 23.8 + - - +
83D ILE 3.1 2.7 + - - +
85D LYS* 1.3 87.5 - - - +
87D LEU* 1.3 60.9 + - - +
89D ARG* 3.2 6.0 + - - +
90D SER* 2.9 32.5 + - - -
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Residues in contact with LEU 87 (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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47C ILE* 5.3 0.7 - - + -
49C LEU* 4.1 19.1 - - + -
53C ASP 3.4 28.5 - - - +
54C LEU* 4.7 1.6 - - - -
66C PHE* 3.8 24.7 - - + -
83D ILE* 2.8 45.1 + - + +
84D LEU* 3.9 3.1 - - - +
86D ASN* 1.3 72.4 - - - +
88D SER* 1.3 62.4 + - - +
90D SER* 3.2 2.9 + - - -
91D ARG 3.1 3.1 + - - -
92D ARG* 3.0 44.9 + - + -
93D LEU* 3.4 32.4 + - + +
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Residues in contact with SER 88 (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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84D LEU 2.8 19.9 + - - -
85D LYS* 3.7 6.3 - - - -
87D LEU* 1.3 78.5 - - - +
89D ARG* 1.3 62.5 + - - +
91D ARG* 3.2 38.6 + - - +
93D LEU* 4.1 5.1 - - - +
95D SER 5.5 1.8 - - - -
96D ASP 3.7 19.5 + - - -
97D LYS* 4.8 5.4 - - - +
98D VAL* 5.6 5.6 - - - -
100D GLN* 4.4 9.1 - - - -
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Residues in contact with ARG 89 (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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85D LYS 2.9 18.3 + - - +
86D ASN* 3.2 7.2 + - - +
88D SER* 1.3 77.2 + - - +
90D SER* 1.3 59.2 + - - +
91D ARG* 3.2 2.7 + - - +
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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