Contacts of the helix formed by residues 70 - 82 (chain A) in PDB entry 5EWL
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 ASN 70 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68A ARG* 3.9 3.3 - - - +
69A PRO* 1.3 77.0 - - - +
71A ALA* 1.4 56.6 + - - +
72A ILE* 3.2 5.8 + - - -
73A GLN* 2.9 40.9 + - - +
74A MET* 3.0 28.9 + - - +
102A LEU* 5.8 5.4 - - - -
118B GLN* 5.2 1.3 - - - +
321B CYS 3.3 15.6 + - - +
322B TYR 3.6 4.6 - - - -
324B THR* 3.1 27.3 + - - +
325B HIS* 3.1 28.6 + - + +
328B ARG* 5.9 0.2 - - - +
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Residues in contact with ALA 71 (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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70A ASN* 1.4 70.9 - - - +
72A ILE* 1.4 59.7 + - - +
74A MET* 3.6 4.5 - - - +
75A ALA* 2.9 24.9 + - - +
102A LEU* 5.9 5.5 - - - +
106A PRO* 3.6 27.2 - - + +
114B PHE* 3.5 14.8 - - + -
118B GLN* 3.4 31.4 - - - +
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Residues in contact with ILE 72 (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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70A ASN* 3.2 7.5 + - - +
71A ALA* 1.4 73.8 - - - +
73A GLN* 1.3 63.6 + - - +
75A ALA* 3.2 4.9 + - - +
76A LEU* 3.0 32.1 + - + +
82B ILE* 3.5 26.9 - - + -
86B CYS* 4.2 1.6 - - - -
114B PHE* 3.8 23.6 - - + -
115B ILE* 4.9 5.4 - - + +
118B GLN* 3.5 27.9 - - + +
119B THR* 3.7 23.3 - - + -
321B CYS* 4.0 33.7 - - + +
322B TYR* 4.5 1.8 - - + -
324B THR* 4.3 4.5 - - + +
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Residues in contact with GLN 73 (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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68A ARG* 3.8 18.5 - - + +
69A PRO* 3.3 32.5 - - + +
70A ASN* 2.9 26.3 + - - +
72A ILE* 1.3 75.1 - - - +
74A MET* 1.4 56.6 + - - +
76A LEU* 3.3 10.7 + - + +
77A SER* 2.8 29.1 + - - -
322B TYR* 3.3 49.4 - - + +
325B HIS* 4.3 0.2 - - - -
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Residues in contact with MET 74 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A VAL* 3.5 43.1 - - + -
65A VAL* 4.0 6.5 - - + -
66A THR 4.5 0.2 - - - +
67A HIS* 3.9 6.1 - - + -
68A ARG* 3.4 31.1 - - + +
70A ASN 3.0 18.7 + - - +
71A ALA* 3.6 9.0 - - - +
72A ILE 3.3 0.2 - - - -
73A GLN* 1.4 72.6 - - - +
75A ALA* 1.3 65.3 + - - +
77A SER* 3.1 19.7 + - - +
78A VAL* 3.1 26.4 + - + +
103A THR 5.6 1.6 - - - +
106A PRO* 4.4 8.3 - - + -
107A ILE* 4.0 19.7 - - + -
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Residues in contact with ALA 75 (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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71A ALA 2.9 13.5 + - - +
72A ILE 3.5 8.3 - - - +
74A MET* 1.3 73.9 - - - +
76A LEU* 1.3 62.3 + - - +
78A VAL* 3.3 14.9 + - - +
79A CYS* 3.4 17.5 + - - -
106A PRO* 4.2 9.1 - - + +
110A THR* 3.8 21.8 + - + +
78B PRO* 6.3 0.2 - - + -
82B ILE* 4.1 21.5 - - + -
114B PHE* 4.3 10.1 - - + -
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Residues in contact with LEU 76 (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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72A ILE* 3.0 37.7 + - + +
73A GLN* 3.6 9.0 - - - +
74A MET 3.2 0.2 - - - -
75A ALA* 1.3 75.8 - - - +
77A SER* 1.3 57.5 + - - +
79A CYS* 3.3 7.0 + - - +
80A GLU* 3.0 43.3 + - - +
79B LYS* 3.8 28.7 - - + +
82B ILE* 4.0 20.2 - - + -
83B THR* 3.7 22.7 - - - +
322B TYR* 4.0 23.3 - - + +
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Residues in contact with SER 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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65A VAL* 3.7 19.2 - - - +
68A ARG* 3.8 20.6 + - - -
73A GLN 2.8 13.2 + - - -
74A MET* 3.1 20.4 + - - -
76A LEU* 1.3 72.4 - - - +
78A VAL* 1.4 58.0 + - - +
80A GLU* 4.6 3.1 - - - -
81A ASP* 2.7 59.9 + - - +
82A LEU* 4.7 1.1 - - - +
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Residues in contact with VAL 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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74A MET* 3.1 21.3 + - + +
75A ALA* 3.3 9.6 + - - +
77A SER* 1.4 74.4 - - - +
79A CYS* 1.3 50.8 + - - +
82A LEU* 2.9 23.8 + - + -
83A ILE* 2.8 52.3 + - + -
90A ILE* 3.8 21.8 - - + -
107A ILE* 4.0 36.8 - - + +
110A THR* 3.8 13.5 - - + -
111A ALA 4.8 1.8 - - - +
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Residues in contact with CYS 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 ALA 3.4 6.7 + - - +
76A LEU* 3.3 9.1 + - - +
77A SER 3.3 0.4 - - - -
78A VAL* 1.3 79.2 - - - +
80A GLU* 1.3 57.2 + - - +
83A ILE* 3.9 2.8 - - - +
84A SER* 3.1 29.5 + - - -
110A THR* 3.6 17.3 - - - -
328A GLY* 4.3 4.9 - - - -
329A CYS* 2.0 54.9 + - + -
78B PRO* 4.7 1.8 - - - -
79B LYS* 4.0 27.8 - - + -
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Residues in contact with GLU 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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76A LEU* 3.0 32.0 + - - +
77A SER* 4.1 2.0 + - - +
79A CYS* 1.3 76.4 - - - +
81A ASP* 1.3 72.4 + - - +
84A SER* 2.7 18.8 + - - -
79B LYS* 2.8 39.6 + - - +
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Residues in contact with ASP 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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63A THR* 3.4 19.6 - - - +
65A VAL* 3.4 28.0 - - + +
68A ARG* 5.3 1.6 + - - -
77A SER* 2.7 43.0 + - - +
80A GLU* 1.3 85.3 - - - +
82A LEU* 1.3 58.1 + - + +
84A SER* 3.6 3.6 + - - -
85A SER* 3.6 8.7 + - - -
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Residues in contact with LEU 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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30A GLY* 4.3 1.3 - - - -
31A ALA 4.0 6.5 - - - +
32A VAL* 3.8 28.5 - - + -
63A THR* 3.8 29.2 - - + +
64A SER* 4.0 16.8 - - - -
65A VAL* 4.4 7.6 - - + +
77A SER 4.7 0.2 - - - +
78A VAL* 2.9 24.0 + - + +
81A ASP* 1.3 85.9 - - + +
83A ILE* 1.3 59.8 + - - +
84A SER 3.1 1.6 - - - -
85A SER* 2.9 17.7 + - - -
86A GLN 3.5 0.7 + - - -
87A VAL* 3.4 33.4 - - + +
90A ILE* 3.9 25.6 - - + -
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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