Contacts of the helix formed by residues 79 - 93 (chain A) in PDB entry 1PS9
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 GLN 79 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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73A MET* 2.7 33.8 + - - +
74A LEU* 3.2 12.7 - - + +
75A ASN* 2.6 38.6 + - - +
76A ASP* 2.6 29.1 + - + +
78A SER* 1.3 74.3 - - - +
80A ILE* 1.3 62.5 + - - +
81A PRO* 3.5 0.9 - - - -
82A HIS* 3.0 25.4 - - + +
83A HIS* 3.1 13.9 - - + +
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Residues in contact with ILE 80 (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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74A LEU* 5.4 1.8 - - + -
76A ASP 4.7 0.4 - - - +
77A ALA* 3.2 38.1 - - + +
79A GLN* 1.3 75.9 - - - +
81A PRO* 1.3 58.2 - - + +
82A HIS 3.1 0.5 + - - -
83A HIS* 3.1 4.6 + - - +
84A ARG* 2.7 68.1 + - - +
149A LEU* 4.1 22.0 - - + +
152A GLU* 3.6 31.0 - - + +
153A ALA* 3.9 18.8 - - + +
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Residues in contact with PRO 81 (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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77A ALA 3.9 2.5 - - - +
78A SER* 3.2 18.2 - - - +
79A GLN 3.7 0.4 - - - -
80A ILE* 1.3 97.1 - - + +
82A HIS* 1.3 60.8 + - - +
84A ARG* 3.6 17.3 - - + +
85A THR* 2.9 28.4 + - - -
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Residues in contact with HIS 82 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A GLU* 4.1 21.8 + - - -
32A TYR 5.5 2.7 - - - -
35A GLY* 4.4 2.9 - - - -
36A ALA* 3.2 49.9 - - + +
39A LEU* 4.8 6.0 - - + +
79A GLN* 3.0 19.2 + - + +
81A PRO* 1.3 82.8 - - - +
83A HIS* 1.3 90.7 + + + +
85A THR* 3.2 16.2 + - - -
86A ILE* 3.6 12.5 + - + +
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Residues in contact with HIS 83 (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 ILE* 3.9 25.8 - - + -
73A MET 4.9 3.8 + - - -
74A LEU* 3.6 30.7 - - + +
79A GLN* 3.1 27.1 - - - +
80A ILE* 3.1 3.2 + - - +
82A HIS* 1.3 92.3 - + - +
84A ARG* 1.3 62.5 + - - +
85A THR 3.1 2.0 - - - -
86A ILE* 2.8 26.7 + - + +
87A THR* 2.9 16.3 + - - +
99A LEU* 4.2 4.7 - - + -
153A ALA* 3.5 22.2 - - + -
155A TYR* 2.8 31.8 + + + -
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Residues in contact with ARG 84 (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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80A ILE* 2.7 45.5 + - + +
81A PRO* 3.6 17.4 - - + +
83A HIS* 1.3 71.4 - - - +
85A THR* 1.3 62.0 + - - +
88A GLU* 3.0 59.3 + - + +
152A GLU* 3.5 24.7 + - - +
153A ALA* 3.5 19.0 + - - +
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Residues in contact with THR 85 (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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36A ALA* 4.1 21.7 - - + +
37A GLU* 3.9 24.7 - - - +
40A ALA* 3.7 5.7 - - + +
81A PRO 2.9 18.6 + - - -
82A HIS* 3.2 11.5 + - - -
83A HIS 3.1 0.2 - - - -
84A ARG* 1.3 76.2 - - - +
86A ILE* 1.3 60.5 + - - +
88A GLU* 4.4 4.1 - - - +
89A ALA* 3.5 20.6 + - - +
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Residues in contact with ILE 86 (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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36A ALA* 3.6 19.7 - - - +
39A LEU* 3.8 30.5 - - + -
40A ALA* 4.1 11.9 - - - +
43A TYR* 3.9 25.8 - - + -
82A HIS* 4.0 26.2 - - + +
83A HIS* 2.8 11.1 + - + +
85A THR* 1.3 75.1 - - - +
87A THR* 1.3 67.0 + - + +
88A GLU 3.1 1.1 - - - -
89A ALA* 3.0 14.2 + - - +
90A VAL* 3.2 13.2 + - + +
97A ILE* 3.9 15.9 - - + -
155A TYR* 4.4 16.2 - - - +
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Residues in contact with THR 87 (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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83A HIS 2.9 18.5 + - - +
84A ARG* 3.4 6.2 + - - -
86A ILE* 1.3 71.6 - - - +
88A GLU* 1.3 62.3 + - - +
90A VAL* 3.4 1.2 + - - +
91A HIS* 2.9 40.5 + - - -
97A ILE* 4.1 11.4 - - + -
153A ALA 2.8 21.1 + - - +
154A GLY* 3.5 16.2 + - - +
155A TYR* 3.6 52.0 - - + +
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Residues in contact with GLU 88 (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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84A ARG* 3.0 48.3 + - + +
85A THR* 4.4 4.3 - - - +
87A THR* 1.3 84.5 + - - +
89A ALA* 1.3 64.4 + - - +
91A HIS* 4.1 8.6 - - - +
92A GLN* 3.0 36.2 + - + +
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Residues in contact with ALA 89 (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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40A ALA* 3.5 31.4 - - + +
44A ALA* 3.7 8.2 - - + +
85A THR 3.5 14.0 + - - +
86A ILE 3.0 8.7 + - - +
88A GLU* 1.3 79.5 - - - +
90A VAL* 1.3 61.4 + - - +
92A GLN* 3.6 6.5 + - - +
93A GLU* 3.4 24.6 + - - +
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Residues in contact with VAL 90 (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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40A ALA 5.2 0.2 - - - +
43A TYR* 3.7 33.4 - - + -
44A ALA* 4.4 2.2 - - - +
47A ALA* 3.9 15.7 - - + +
54A ILE* 4.7 2.7 - - + -
86A ILE* 3.2 13.0 + - + +
87A THR 3.7 6.7 - - - +
89A ALA* 1.3 76.1 - - + +
91A HIS* 1.3 64.5 + - + +
93A GLU* 3.1 10.7 + - - +
94A GLY 3.3 0.2 + - - -
95A GLY* 3.1 43.6 + - - +
96A LYS* 3.6 19.5 - - - +
97A ILE* 4.2 20.9 - - + -
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Residues in contact with HIS 91 (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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87A THR* 2.9 28.8 + - - +
88A GLU* 4.1 8.9 + - - +
89A ALA 3.4 0.2 - - - -
90A VAL* 1.3 75.0 - - + +
92A GLN* 1.3 64.9 + - + +
94A GLY* 2.9 18.7 + - - -
95A GLY 3.4 22.0 - - - -
96A LYS* 4.5 0.7 - - - -
97A ILE* 4.8 1.6 - - - +
154A GLY* 3.0 27.8 - - - -
156A ASP* 2.8 30.6 + - - -
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Residues in contact with GLN 92 (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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88A GLU* 3.0 30.3 + - + +
89A ALA* 3.8 8.3 - - - +
90A VAL 3.3 0.2 - - - -
91A HIS* 1.3 79.4 - - - +
93A GLU* 1.3 67.5 + - + +
94A GLY 3.2 0.9 + - - -
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Residues in contact with GLU 93 (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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17A LYS* 4.8 2.3 + - - -
44A ALA* 3.6 25.0 - - + +
47A ALA* 3.8 12.5 - - + +
48A ARG* 3.3 51.6 - - - +
89A ALA 3.4 15.0 - - - +
90A VAL 3.1 7.5 + - - +
91A HIS 3.1 0.6 - - - -
92A GLN* 1.3 83.0 - - + +
94A GLY* 1.3 60.6 + - - +
95A GLY 3.4 0.2 - - - -
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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