Contacts of the helix formed by residues 83 - 90 (chain A) in PDB entry 3D9L
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 83 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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37A ILE* 4.0 26.4 - - + +
40A TYR* 3.7 50.0 - - + +
73A SER* 4.5 0.6 + - - -
81A LYS 3.3 12.3 + - - +
82A ASP* 1.3 72.7 + - - +
84A PHE* 1.3 68.4 + - + +
85A ALA 3.7 0.2 - - - -
86A PRO* 3.8 6.4 - - - +
87A ARG* 3.3 25.3 + - - +
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Residues in contact with PHE 84 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A ALA 3.6 25.1 - - - -
34A ILE* 3.8 18.8 - - + -
37A ILE* 4.0 21.3 - - + -
40A TYR* 3.7 26.9 - - + -
43A VAL* 3.7 23.8 - - + -
44A VAL* 4.1 14.8 - - + -
69A ILE* 3.4 24.7 - - + -
70A VAL* 4.0 8.7 - - + -
73A SER* 3.3 24.0 - - - +
82A ASP* 2.9 10.6 + - - +
83A VAL* 1.3 80.0 - - + +
85A ALA* 1.3 59.7 - - - +
87A ARG* 3.3 2.9 + - - +
88A PHE* 2.9 38.1 + + + -
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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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70A VAL* 3.3 29.0 - - + +
74A ARG* 4.8 2.5 - - - +
82A ASP* 3.0 22.3 + - - +
84A PHE* 1.3 72.9 - - - +
86A PRO* 1.4 66.2 - - + +
88A PHE 3.4 0.3 + - - -
89A SER* 2.9 19.6 + - - -
122A VAL 3.8 18.8 - - - +
123A PHE* 3.2 21.9 - - + -
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Residues in contact with PRO 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 ASP* 3.3 27.6 - - - +
83A VAL* 3.8 5.8 - - - +
84A PHE 3.7 2.0 - - - -
85A ALA* 1.4 94.1 - - + +
87A ARG* 1.3 59.5 + - - +
89A SER* 2.5 26.5 + - - +
90A ASN* 3.5 8.8 - - - +
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Residues in contact with ARG 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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40A TYR* 3.9 16.8 - - + -
41A LYS* 3.6 55.4 + - - +
44A VAL* 3.5 32.9 - - + +
48A GLU* 4.5 1.7 - - - +
83A VAL 3.3 17.3 + - - +
84A PHE 3.3 3.4 + - - +
86A PRO* 1.3 74.2 - - - +
88A PHE* 1.3 65.3 + - - +
89A SER 3.1 1.9 + - - -
90A ASN* 3.4 39.7 + - - +
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Residues in contact with PHE 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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43A VAL 5.2 0.4 - - - -
44A VAL* 3.7 39.2 - - + +
47A VAL* 3.8 33.7 - - + -
48A GLU* 4.1 12.6 - - + +
66A ILE* 3.8 38.8 - - + -
69A ILE* 4.2 20.9 - - + -
70A VAL* 3.6 23.1 - - + -
84A PHE* 2.9 30.8 + + - +
85A ALA 3.8 3.8 - - - +
87A ARG* 1.3 72.5 - - - +
89A SER* 1.3 61.2 + - - +
90A ASN 3.4 0.2 + - - -
91A ASN 3.7 1.7 + - - -
92A ILE* 3.2 27.4 + - + +
95A THR* 5.2 0.6 + - - -
123A PHE* 4.4 12.6 - - + -
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Residues in contact with SER 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 2.9 13.7 + - - -
86A PRO* 2.5 23.2 + - - +
87A ARG 3.1 0.8 - - - -
88A PHE* 1.3 76.3 - - - +
90A ASN* 1.3 69.7 + - - +
92A ILE* 3.3 23.4 - - - +
93A ILE* 5.9 0.2 - - - +
123A PHE* 4.3 11.9 - - - -
127A ILE* 4.3 25.9 - - - +
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Residues in contact with ASN 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 PRO 3.5 10.3 - - - +
87A ARG* 3.6 44.9 + - - +
88A PHE 3.3 0.4 - - - -
89A SER* 1.3 81.5 + - - +
91A ASN* 1.3 71.6 + - - +
92A ILE 3.9 0.2 + - - -
93A ILE* 6.2 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