Contacts of the helix formed by residues 100 - 104 (chain A) in PDB entry 3SDI
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 TYR 100 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95A VAL 4.8 1.6 - - - +
96A ALA 3.3 12.4 + - - +
97A HIS 3.3 2.0 + - - -
98A THR 3.5 0.4 - - - -
99A SER* 1.3 82.5 - - - +
101A LYS* 1.3 62.0 + - - +
102A ARG* 3.1 4.7 + - - +
103A TYR* 2.9 58.0 + + - +
105A GLU* 3.2 37.0 + - + +
106A TYR 3.6 7.6 - - - -
107A PRO* 3.4 34.3 - - + -
108A PRO* 3.5 17.5 - - + +
111A LEU* 4.1 10.3 - - + -
66I TYR* 4.0 9.4 + - - -
70I GLU* 2.5 36.0 + - - -
72I ARG* 5.1 1.2 + - - -
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Residues in contact with LYS 101 (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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96A ALA 3.1 12.6 + - - +
97A HIS* 3.1 24.2 + - + +
100A TYR* 1.3 74.6 - - - +
102A ARG* 1.3 64.4 + - + +
104A GLY* 2.9 37.4 + - - -
105A GLU* 3.3 25.1 + - - +
106A TYR* 3.6 47.5 + - + -
36H ARG* 5.7 4.6 - - - +
57H GLN* 5.4 9.5 + - - +
60H GLY 6.3 0.4 - - - -
61H SER* 5.6 7.1 - - - +
64H GLU* 4.5 6.3 + - - -
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Residues in contact with ARG 102 (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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94A LYS* 5.8 1.8 - - - +
97A HIS* 2.9 24.4 + - + +
98A THR* 4.1 28.7 - - - +
101A LYS* 1.3 76.5 - - + +
102A ILE* 1.3 62.3 + - - +
57H GLN 5.8 1.6 - - - +
58H LEU* 4.0 27.4 - - - +
61H SER* 3.0 33.5 + - - +
62H ASN* 3.0 28.9 + - - +
65H LEU* 4.1 14.1 - - - +
85I SER* 3.6 17.0 - - - -
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Residues in contact with ILE 102 (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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98A THR 4.4 11.0 + - - -
99A SER* 4.0 21.5 + - - +
100A TYR* 3.1 8.2 + - - +
101A LYS 3.0 0.8 - - - -
102A ARG* 1.3 85.6 - - - +
103A TYR* 1.3 81.7 + - + +
104A GLY 3.6 0.7 - - - -
81I GLN* 3.3 11.3 + - - +
82I LEU* 3.6 29.7 - - - +
85I SER* 2.8 23.9 + - - -
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Residues in contact with TYR 103 (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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99A SER 4.7 4.0 - - - -
100A TYR* 2.9 59.1 + + + +
102A ILE* 1.3 97.0 + - + +
104A GLY* 1.3 57.8 + - - +
105A GLU* 3.0 29.5 + - + +
62I LYS* 5.0 2.9 + - - +
66I TYR* 3.5 33.9 + + + +
70I GLU* 4.8 0.2 - - - -
74I ILE* 4.4 3.1 - - + -
78I THR* 3.7 27.7 - - + +
81I GLN* 3.4 25.1 - - - +
82I LEU* 3.9 24.7 - - + +
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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