Contacts of the helix formed by residues 76 - 91 (chain A) in PDB entry 3PEI
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 GLU 76 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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73A ILE* 3.0 32.9 + - + +
74A ALA 3.0 1.2 - - - -
75A SER* 1.3 85.5 + - - +
77A TYR* 1.3 62.6 + - - +
78A ASP 3.3 2.9 - - - -
79A LYS* 2.9 61.6 + - + +
80A ILE* 3.5 10.7 + - + +
371A ALA* 5.5 6.8 - - - +
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Residues in contact with TYR 77 (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 ILE* 3.6 8.7 - - + +
66A LEU* 3.9 23.1 - - + -
72A PHE* 3.9 23.3 - + + -
73A ILE 3.9 1.3 + - - -
74A ALA* 3.0 19.3 + - - +
75A SER 3.4 0.8 - - - -
76A GLU* 1.3 77.1 - - - +
78A ASP* 1.3 65.7 + - - +
80A ILE* 3.0 13.3 + - + +
81A ILE* 2.9 52.8 + - + +
112A PHE* 3.3 24.8 - + - -
115A ASP* 4.1 19.5 - - + -
116A THR* 2.8 43.5 + - - -
118A ARG* 5.8 0.4 - - - -
119A ALA* 4.8 1.8 - - + -
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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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75A SER 4.9 4.8 + - - +
76A GLU 3.3 1.5 + - - -
77A TYR* 1.3 77.9 + - - +
79A LYS* 1.3 62.7 + - + +
82A ALA* 2.8 30.4 + - - +
118A ARG* 2.7 44.2 + - - -
119A ALA* 3.7 20.1 - - - +
122A SER* 4.5 4.5 + - - -
123A GLU* 3.6 24.8 - - - +
166A GLN* 5.0 2.6 + - - -
501A FMT 4.6 7.5 - - - +
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Residues in contact with LYS 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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75A SER 5.4 2.0 - - - +
76A GLU* 2.9 55.1 + - + +
78A ASP* 1.3 83.5 - - + +
80A ILE* 1.3 63.6 + - + +
82A ALA* 3.4 18.2 - - - +
83A LYS* 3.7 15.2 + - - +
370A ASP* 5.2 11.0 + - - -
504A EDO 5.4 8.3 - - - -
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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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48A SER* 3.3 26.9 - - - +
49A GLY* 4.0 10.3 - - - +
64A LEU* 3.6 31.5 - - + +
65A GLY 3.8 12.3 - - - +
66A LEU* 4.3 12.3 - - + -
72A PHE* 4.0 27.1 - - + -
73A ILE 5.9 0.4 - - - +
76A GLU* 3.5 13.4 + - + +
77A TYR* 3.0 13.1 + - + +
79A LYS* 1.3 75.6 - - + +
81A ILE* 1.3 66.8 + - - +
82A ALA 3.1 1.3 - - - -
83A LYS* 3.0 24.7 + - - +
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Residues in contact with ILE 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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15A LEU* 5.3 2.0 - - + -
17A ILE* 4.3 8.7 - - + -
64A LEU* 3.9 19.5 - - + -
77A TYR* 2.9 54.5 + - + +
78A ASP 3.9 1.8 - - - +
80A ILE* 1.3 74.5 - - - +
82A ALA* 1.3 64.3 + - - +
84A ALA* 2.9 6.3 + - + +
85A ALA* 2.9 18.1 + - + +
116A THR* 4.9 6.5 - - + +
119A ALA* 3.8 22.4 - - + +
120A LEU* 3.7 45.5 - - + +
123A GLU* 4.6 3.6 - - + -
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Residues in contact with ALA 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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78A ASP 2.8 19.1 + - - +
79A LYS* 3.4 13.0 - - - +
80A ILE 3.1 0.4 - - - -
81A ILE* 1.3 76.7 - - - +
83A LYS* 1.3 62.0 + - + +
85A ALA* 3.1 3.5 + - - +
86A GLU* 3.0 34.9 + - + +
123A GLU* 3.6 28.9 - - - +
461A LYS* 6.1 0.7 - - - +
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Residues in contact with LYS 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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49A GLY* 3.4 24.0 - - - +
51A VAL* 3.5 22.6 - - + +
79A LYS 3.8 11.9 - - - +
80A ILE 3.0 13.8 + - - +
82A ALA* 1.3 78.5 - - + +
84A ALA* 1.3 61.7 + - - +
86A GLU* 3.5 32.9 + - - +
87A GLN* 3.5 15.6 + - - +
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Residues in contact with ALA 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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15A LEU* 3.9 37.9 - - + -
51A VAL* 4.1 7.7 - - - +
62A ILE* 5.0 2.6 - - + +
64A LEU* 4.2 15.5 - - + +
80A ILE 3.8 1.0 + - - -
81A ILE* 2.9 9.2 + - + +
83A LYS* 1.3 76.4 - - - +
85A ALA* 1.3 62.3 + - - +
87A GLN* 3.0 10.3 + - - +
88A LEU* 2.9 32.7 + - + +
120A LEU* 5.2 3.1 - - + -
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Residues in contact with ALA 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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81A ILE 2.9 12.0 + - - +
82A ALA 3.1 8.0 + - - +
84A ALA* 1.3 77.0 - - - +
86A GLU* 1.3 62.0 + - - +
88A LEU* 3.3 9.0 + - + +
89A LYS* 3.0 23.6 + - - +
120A LEU* 5.0 4.7 - - + +
123A GLU* 3.6 26.5 - - + +
124A THR* 3.6 29.7 - - + +
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Residues in contact with GLU 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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82A ALA* 3.0 28.6 + - + +
83A LYS* 3.8 30.4 + - - +
84A ALA 3.2 0.2 - - - -
85A ALA* 1.3 75.2 - - - +
87A GLN* 1.3 64.2 + - - +
89A LYS* 3.3 5.9 + - - +
90A LYS* 2.8 32.2 + - - +
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Residues in contact with GLN 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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51A VAL* 3.6 28.5 - - + +
53A PRO* 3.8 14.6 - - + +
62A ILE* 4.2 17.5 - - + -
83A LYS 3.5 7.6 + - - +
84A ALA* 3.0 8.8 + - - +
86A GLU* 1.3 81.4 + - - +
88A LEU* 1.3 60.1 + - - +
90A LYS* 3.8 16.5 - - - +
91A LEU* 2.8 43.5 + - + +
512A EDO 3.3 41.8 + - - -
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Residues in contact with LEU 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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15A LEU* 5.2 4.7 - - + -
62A ILE* 3.8 22.2 - - + -
84A ALA* 2.9 20.2 + - + +
85A ALA* 3.6 11.0 - - - +
87A GLN* 1.3 76.2 - - - +
89A LYS* 1.3 56.8 + - - +
91A LEU 3.7 0.2 - - - -
92A ALA* 2.9 23.4 + - - -
93A ILE* 2.9 29.8 + - + +
96A ILE* 3.8 28.5 - - + -
120A LEU* 3.8 29.4 - - + -
124A THR* 4.5 8.1 - - + -
137A TYR* 3.3 15.8 - - - +
139A LEU* 4.5 13.2 - - + -
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Residues in contact with LYS 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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85A ALA 3.0 13.6 + - - +
86A GLU* 3.7 8.3 - - - +
88A LEU* 1.3 75.2 - - - +
90A LYS* 1.3 64.5 + - - +
92A ALA* 3.0 15.1 + - - +
124A THR* 6.1 0.7 - - + -
125A TYR 5.8 0.8 + - - -
126A VAL* 4.5 13.9 - - - +
135A GLU* 2.9 38.2 + - - +
137A TYR* 3.8 37.5 + - + +
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Residues in contact with LYS 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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86A GLU 2.8 21.4 + - - +
87A GLN* 3.8 23.6 - - - +
89A LYS* 1.3 77.4 - - - +
91A LEU* 1.3 74.2 + - + +
92A ALA* 3.5 1.2 + - - +
512A EDO 3.3 24.0 - - - +
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Residues in contact with LEU 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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53A PRO* 4.2 18.8 - - + -
55A LEU* 4.3 20.2 - - + -
60A ILE* 4.3 20.6 - - + +
62A ILE* 4.4 5.6 - - + -
87A GLN* 2.8 36.0 + - - +
90A LYS* 1.3 91.9 - - + +
92A ALA* 1.3 70.9 + - - +
93A ILE* 3.2 28.3 + - + +
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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