Contacts of the strand formed by residues 90 - 96 (chain C) in PDB entry 4A12
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 LYS 90 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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84C GLN* 4.2 25.4 + - - +
85C VAL 3.8 0.3 - - - -
86C ASN* 2.8 36.0 + - + +
89C VAL* 1.4 85.3 - - + +
91C ALA* 1.3 63.4 + - - +
92C GLN* 5.4 4.5 - - - +
125C LEU* 3.6 2.9 - - - -
153C GLU* 4.2 19.5 + - - -
154C ALA 3.3 14.6 - - - +
155C ARG* 3.7 38.4 - - + +
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Residues in contact with ALA 91 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84C GLN* 3.3 13.2 - - - +
85C VAL* 3.7 18.2 - - + -
90C LYS* 1.3 77.8 - - - +
92C GLN* 1.3 60.3 + - - +
121C LEU* 3.8 18.3 - - + +
125C LEU* 3.8 23.5 - - + +
153C GLU* 3.4 4.2 - - - +
154C ALA 2.8 34.5 + - - +
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Residues in contact with GLN 92 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82C LEU* 3.6 2.9 - - - +
83C ILE* 2.8 45.5 + - + +
84C GLN* 2.8 34.7 + - + +
90C LYS* 5.4 5.3 - - - +
91C ALA* 1.3 74.1 - - - +
93C SER* 1.3 64.9 + - - +
94C ILE* 4.4 5.2 - - - +
121C LEU* 3.7 2.9 - - - -
151C ARG* 3.3 42.0 - - + +
152C ALA 3.2 13.2 - - - +
153C GLU* 3.7 19.2 + - + +
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Residues in contact with SER 93 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78C PHE* 3.9 19.9 - - - -
81C ASP 3.2 12.3 - - - -
82C LEU* 4.2 0.4 - - - -
83C ILE 4.3 0.2 - - - +
92C GLN* 1.3 74.0 - - - +
94C ILE* 1.3 68.4 + - - +
117C GLN* 3.2 30.9 + - - +
121C LEU* 3.7 23.5 - - - +
151C ARG* 3.7 0.5 - - - -
152C ALA 2.9 32.3 + - - +
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Residues in contact with ILE 94 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80C GLY* 3.2 3.8 - - - -
81C ASP* 2.7 47.4 + - + +
83C ILE* 3.4 33.4 - - + -
92C GLN* 4.4 13.7 - - - +
93C SER* 1.3 80.1 - - - +
95C LEU* 1.3 60.3 + - - +
96C ASP* 5.9 0.7 - - + +
117C GLN* 3.5 1.1 - - - -
149C THR* 4.5 19.7 - - + -
150C VAL 3.3 5.4 - - - +
151C ARG* 4.4 11.7 - - + -
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Residues in contact with LEU 95 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79C ILE* 4.2 5.6 - - + -
80C GLY* 3.8 24.0 - - - +
81C ASP* 5.5 0.9 - - - -
94C ILE* 1.3 75.2 - - - +
96C ASP* 1.3 68.8 + - - +
97C ILE* 3.5 23.8 + - + -
101C SER* 5.9 0.9 - - - +
113C VAL* 3.9 23.3 - - + +
114C LEU* 5.3 1.3 - - + +
117C GLN* 3.5 37.9 - - + +
148C ASP 3.8 0.3 - - - +
149C THR* 3.4 3.2 - - - +
150C VAL* 2.8 40.2 + - + +
74D GLU* 4.2 19.5 - - + +
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Residues in contact with ASP 96 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81C ASP* 5.8 1.0 + - - -
94C ILE* 4.3 1.2 - - + +
95C LEU* 1.3 83.2 - - - +
97C ILE* 1.3 63.2 + - - +
98C THR* 3.3 29.4 + - + +
101C SER* 4.8 2.6 + - - -
147C ASN* 3.9 11.9 - - - +
148C ASP 3.8 6.4 - - - +
149C THR* 3.1 26.7 + - + +
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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