Contacts of the helix formed by residues 75 - 83 (chain A) in PDB entry 3W8I
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 75 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74A VAL* 1.3 77.0 - - - +
76A PHE* 1.3 67.0 + - - +
77A THR* 3.4 6.6 + - - +
78A GLU* 3.1 42.0 + - - +
79A SER* 3.0 25.7 + - - -
188A ILE* 3.3 29.9 - - - +
191A PHE* 4.7 0.6 - - - -
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Residues in contact with PHE 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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21A PRO* 4.1 21.5 - - + -
25A VAL* 4.9 1.6 - - + -
60A GLN* 3.3 46.0 - - + -
63A ILE* 3.6 30.3 - - + -
64A MET* 3.7 30.5 - - + -
67A LEU* 4.5 5.6 - - + -
74A VAL 3.4 4.9 + - - -
75A ASN* 1.3 75.5 - - - +
77A THR* 1.3 65.7 - - + +
79A SER* 3.3 3.6 + - - -
80A LEU* 2.9 51.6 + - + +
407B PHE* 3.8 25.3 - + - -
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Residues in contact with THR 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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60A GLN* 5.1 5.6 - - - +
64A MET* 6.4 0.2 - - - -
75A ASN* 3.4 15.3 - - - +
76A PHE* 1.3 84.5 - - + +
78A GLU* 1.3 60.3 + - - +
80A LEU* 3.9 8.1 - - - -
81A LEU* 2.9 25.6 + - - +
188A ILE* 3.6 17.1 - - + +
191A PHE* 3.4 20.4 - - - +
192A VAL* 4.1 13.9 + - + +
195A ASN* 3.1 19.2 + - - +
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Residues in contact with GLU 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 VAL* 5.4 6.5 - - - +
75A ASN* 3.1 31.5 + - + +
76A PHE 3.3 0.2 - - - -
77A THR* 1.3 81.3 + - - +
79A SER* 1.3 58.4 + - - +
81A LEU* 3.2 7.3 + - - +
82A ARG* 2.9 60.7 + - - +
118A PRO* 3.8 20.3 - - + +
191A PHE* 3.9 30.8 - - + -
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Residues in contact with SER 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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74A VAL* 3.2 26.3 - - - +
75A ASN 3.0 16.3 + - - -
76A PHE 3.7 0.7 - - - -
78A GLU* 1.3 75.1 - - - +
80A LEU* 1.3 65.7 + - - +
82A ARG* 3.1 15.9 + - - +
83A MET* 2.9 33.0 + - - +
407B PHE* 3.5 30.6 + - - -
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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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20A MET* 4.2 26.0 - - + +
21A PRO* 4.7 9.2 - - + -
24A ALA* 4.0 26.5 - - + -
25A VAL* 4.3 12.8 - - + -
60A GLN* 5.8 0.2 - - - +
76A PHE* 2.9 47.7 + - + +
77A THR* 3.4 7.4 - - - +
79A SER* 1.3 76.2 - - - +
81A LEU* 1.3 61.1 + - - +
83A MET* 3.2 11.2 + - + +
84A ALA* 3.1 25.1 + - - +
195A ASN* 3.7 20.2 - - + +
407B PHE* 4.6 2.0 - - - -
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Residues in contact with LEU 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 THR 2.9 14.2 + - - +
78A GLU* 3.4 9.0 - - - +
80A LEU* 1.3 77.2 - - - +
82A ARG* 1.3 52.0 + - - +
84A ALA* 3.3 5.2 + - - +
114A LEU 3.3 23.1 - - - +
115A SER* 2.5 30.2 + - - -
117A ILE* 4.0 2.9 - - + -
118A PRO* 3.7 24.0 - - + -
191A PHE* 3.7 27.4 - - + -
194A ALA* 3.8 26.7 - - + -
195A ASN* 3.2 21.0 + - - +
198A ILE* 3.8 18.8 - - + -
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Residues in contact with ARG 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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74A VAL* 6.0 2.6 - - - +
78A GLU* 2.9 48.0 + - - +
79A SER* 3.1 16.2 + - - +
81A LEU* 1.3 77.0 - - - +
83A MET* 1.3 57.2 + - + +
85A ALA* 4.7 1.6 + - - +
115A SER* 3.3 22.5 + - - +
116A LYS* 5.3 4.0 + - - -
118A PRO* 3.6 26.8 + - + +
119A ASP* 2.3 39.4 + - - +
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Residues in contact with MET 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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24A ALA* 4.2 17.4 - - - +
25A VAL* 3.8 24.2 - - - -
79A SER* 2.9 19.3 + - - +
80A LEU* 3.4 16.6 - - + +
82A ARG* 1.3 74.4 - - + +
84A ALA* 1.3 59.2 + - - +
85A ALA 3.4 4.5 + - - -
86A ASP* 4.1 17.8 + - - +
406B LYS* 3.6 54.6 + - + +
407B PHE* 4.0 23.8 - - + -
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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