Contacts of the helix formed by residues 76 - 89 (chain A) in PDB entry 1PRX
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 VAL 76 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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17A ASN* 3.7 20.6 - - - +
18A THR 3.4 25.4 - - - +
19A THR* 3.7 18.8 - - + +
75A SER* 1.3 72.6 - - - +
77A GLU* 1.3 69.8 + - + +
79A HIS* 3.1 10.6 + - + +
80A LEU* 2.9 31.6 + - + +
104A ASP* 2.8 23.6 + - + +
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Residues in contact with GLU 77 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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75A SER* 3.1 8.2 - - - -
76A VAL* 1.3 86.8 - - + +
78A ASP* 1.3 64.3 + - - +
80A LEU* 3.2 15.8 + - + +
81A ALA* 3.1 20.3 + - - +
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Residues in contact with ASP 78 (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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42A ASP* 3.2 13.9 - - + +
43A PHE* 3.9 19.5 - - + -
74A ASP* 4.1 16.0 - - + +
75A SER* 3.1 21.5 + - - +
77A GLU* 1.3 77.8 - - - +
79A HIS* 1.3 55.4 + - - +
81A ALA* 3.1 7.8 + - - +
82A TRP* 2.7 36.9 + - - +
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Residues in contact with HIS 79 (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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19A THR* 3.4 15.7 - - + -
42A ASP* 2.8 41.8 + - - -
72A SER* 3.4 18.2 - - - -
74A ASP 3.2 25.7 + - - -
75A SER 2.9 12.2 + - - -
76A VAL* 3.1 13.0 + - - +
78A ASP* 1.3 76.0 - - - +
80A LEU* 1.3 52.3 + - - +
82A TRP* 3.3 4.8 + - - +
83A SER* 2.8 37.4 + - - -
102A ILE* 3.4 31.2 - - + +
103A ILE 2.7 31.2 + - - -
104A ASP* 3.8 4.7 - - - -
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Residues in contact with LEU 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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19A THR* 4.0 32.5 - - + +
76A VAL* 2.9 26.2 + - + +
77A GLU* 3.4 16.4 - - + +
79A HIS* 1.3 73.9 - - - +
81A ALA* 1.3 65.9 + - - +
83A SER* 3.2 13.9 + - - -
84A LYS 3.6 1.4 + - - -
96A GLU* 3.2 61.2 - - + +
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Residues in contact with ALA 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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43A PHE* 3.9 15.9 - - + -
77A GLU 3.1 11.1 + - - +
78A ASP* 3.1 12.0 + - - +
80A LEU* 1.3 76.1 - - - +
82A TRP* 1.3 61.5 + - - +
84A LYS* 3.2 32.3 + - - +
85A ASP* 3.6 8.7 + - - +
96A GLU* 4.9 2.0 + - - -
213B SER* 5.4 2.8 - - - -
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Residues in contact with TRP 82 (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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39A HIS* 4.5 2.7 - + + -
41A ARG 3.9 11.2 - - - -
42A ASP* 3.3 31.9 - - - +
43A PHE* 3.3 41.0 - + + +
44A THR* 3.9 6.5 - - - -
47A CSO 3.9 9.6 - - + -
48A THR* 2.8 44.1 + - - -
51A LEU* 3.4 27.6 - - + -
72A SER* 3.8 13.5 - - - -
78A ASP 2.7 20.7 + - - +
79A HIS* 3.6 4.0 - - - +
81A ALA* 1.3 72.8 - - - +
83A SER* 1.3 56.4 + - - +
85A ASP* 3.2 3.7 + - + -
86A ILE* 2.9 38.6 + - + +
102A ILE* 4.4 12.6 - - + -
217B TYR* 3.6 16.0 + - - -
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Residues in contact with SER 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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19A THR* 4.9 3.8 - - - +
79A HIS 2.8 18.6 + - - -
80A LEU* 3.3 12.3 - - - -
81A ALA 3.1 0.4 - - - -
82A TRP* 1.3 75.5 - - - +
84A LYS* 1.3 59.7 + - - +
86A ILE* 3.6 11.3 - - - +
87A ASN* 3.0 33.3 + - - +
95A THR 3.6 1.8 - - - -
96A GLU* 3.8 23.6 + - - -
98A LEU* 3.5 23.0 - - - +
102A ILE* 4.0 6.9 - - - +
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Residues in contact with LYS 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 LEU 3.7 3.6 - - - +
81A ALA* 3.2 17.2 + - - +
83A SER* 1.3 76.8 - - - +
85A ASP* 1.3 57.0 + - - +
87A ASN* 3.3 1.2 + - - +
88A ALA* 2.9 28.6 + - - +
94A PRO* 3.2 34.4 - - + +
95A THR* 3.3 10.3 - - - +
96A GLU* 3.6 33.9 + - + +
212B PRO* 4.2 16.7 - - + +
213B SER 6.1 0.2 - - - +
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Residues in contact with ASP 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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43A PHE* 3.5 10.4 - - - -
48A THR* 4.8 2.5 - - + -
81A ALA 3.6 4.0 + - - +
82A TRP* 3.2 10.0 + - + +
84A LYS* 1.3 75.0 - - - +
86A ILE* 1.3 55.6 + - - +
88A ALA* 3.2 2.1 + - - +
89A TYR* 2.7 35.4 + - - +
211B LEU* 3.7 15.1 - - + +
212B PRO* 3.1 14.7 - - - +
213B SER* 2.7 50.3 + - - -
217B TYR* 2.8 31.1 + - - +
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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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48A THR* 4.1 17.3 - - + +
51A LEU* 3.8 37.0 - - + +
52A GLY* 3.8 26.2 - - - +
55A ALA* 5.0 0.9 - - + -
82A TRP* 2.9 40.3 + - + +
83A SER* 3.6 12.6 - - - +
85A ASP* 1.3 76.0 - - - +
87A ASN* 1.3 61.7 + - - +
89A TYR* 3.3 10.4 + - - +
90A ASN* 3.3 23.6 + - - +
98A LEU* 4.1 25.1 - - + -
102A ILE* 4.6 1.8 - - + -
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Residues in contact with ASN 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 SER 3.0 11.3 + - - +
84A LYS 3.6 8.5 - - - +
86A ILE* 1.3 72.6 - - - +
88A ALA* 1.3 60.6 + - - +
90A ASN* 3.0 18.4 + - - +
92A GLU* 2.8 43.2 + - + +
93A GLU 3.4 22.8 + - - +
94A PRO* 3.9 1.3 - - + -
95A THR* 2.8 25.6 + - - +
97A LYS 3.2 21.9 + - - +
98A LEU* 3.8 10.3 - - - +
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Residues in contact with ALA 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 LYS 2.9 17.1 + - - +
85A ASP 3.5 2.5 - - - +
87A ASN* 1.3 73.3 - - - +
89A TYR* 1.3 61.7 + - - +
91A SER* 2.9 18.6 + - - +
92A GLU 3.9 9.4 - - - +
94A PRO* 4.4 5.1 - - + +
209B LYS* 4.0 16.7 + - - +
210B GLU 5.3 1.8 - - - +
211B LEU* 4.4 5.2 - - + -
212B PRO* 3.5 30.5 - - + -
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Residues in contact with TYR 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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48A THR* 4.1 12.8 - - + -
49A THR* 3.6 43.7 + - + +
52A GLY* 3.9 14.8 - - - -
53A ARG* 4.6 1.3 - - + +
85A ASP 2.7 13.6 + - - +
86A ILE* 3.4 11.0 - - - +
87A ASN 3.2 0.2 - - - -
88A ALA* 1.3 76.5 - - - +
90A ASN* 1.3 76.1 + - - +
91A SER* 3.4 6.4 + - - -
178B PRO* 5.8 0.5 - - - +
179B VAL* 4.2 6.6 - - - +
209B LYS* 4.7 13.8 - - + +
211B LEU* 4.7 2.0 - - - +
218B LEU* 4.0 21.3 - - + -
220B TYR* 3.5 22.7 + - - -
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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