Contacts of the strand formed by residues 90 - 96 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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84A GLN* 3.2 16.3 + - - +
86A ASN* 2.8 33.3 + - + +
89A VAL* 1.4 87.7 - - + +
91A ALA* 1.3 61.4 + - - +
92A GLN* 3.8 33.6 - - - +
125A LEU* 3.5 2.7 - - - +
153A GLU* 4.2 17.2 + - - -
154A ALA 3.3 13.2 - - - +
155A ARG* 3.7 22.4 - - + +
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Residues in contact with ALA 91 (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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84A GLN* 3.3 13.0 - - - +
85A VAL* 3.8 15.9 - - + -
90A LYS* 1.3 75.1 - - - +
92A GLN* 1.3 64.0 + - - +
121A LEU* 3.8 19.6 - - + +
125A LEU* 3.8 24.0 - - + -
153A GLU* 3.4 2.9 - - - +
154A ALA 2.8 35.1 + - - +
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Residues in contact with GLN 92 (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 LEU* 3.5 5.0 - - - +
83A ILE* 2.8 40.5 + - + +
84A GLN* 2.8 34.2 + - + +
90A LYS* 3.8 20.2 - - - +
91A ALA* 1.3 79.2 - - - +
93A SER* 1.3 60.6 + - - +
121A LEU* 3.7 2.7 - - - -
151A ARG* 3.5 25.6 + - + +
152A ALA 3.3 4.6 - - - +
153A GLU* 3.0 36.3 + - + +
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Residues in contact with SER 93 (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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78A PHE* 4.0 17.5 - - - -
81A ASP 3.2 15.3 - - - -
82A LEU* 4.2 0.4 - - - -
83A ILE* 4.1 5.6 - - - +
92A GLN* 1.3 75.2 - - - +
94A ILE* 1.3 59.5 + - - +
117A GLN* 3.2 30.1 + - - +
121A LEU* 3.7 22.5 - - - +
150A VAL 3.6 0.3 - - - +
151A ARG* 3.7 2.6 - - - +
152A ALA* 2.9 33.2 + - - +
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Residues in contact with ILE 94 (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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80A GLY* 3.4 1.2 - - - -
81A ASP* 2.7 59.2 + - + +
83A ILE* 3.5 22.4 - - + +
93A SER* 1.3 71.5 - - - +
95A LEU* 1.3 60.7 + - - +
96A ASP* 4.3 7.6 - - - +
117A GLN* 3.7 1.1 - - - -
149A THR* 3.4 29.6 - - + +
150A VAL 3.4 1.8 - - - +
151A ARG* 3.8 37.0 - - + -
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Residues in contact with LEU 95 (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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79A ILE* 4.3 7.6 - - + -
80A GLY* 3.7 24.2 - - - +
94A ILE* 1.3 75.5 - - - +
96A ASP* 1.3 68.3 + - - +
97A ILE* 3.5 25.3 + - + +
101A SER* 5.6 3.8 - - - +
113A VAL* 3.9 23.3 - - + +
114A LEU* 5.3 1.6 - - + +
117A GLN* 3.5 39.3 - - + +
149A THR* 3.4 3.1 - - - -
150A VAL* 2.8 41.4 + - + +
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Residues in contact with ASP 96 (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 ILE* 4.9 7.3 - - - +
95A LEU* 1.3 79.2 - - - +
97A ILE* 1.3 61.3 + - - +
98A THR* 3.1 16.2 + - - +
101A SER* 4.8 1.4 + - - -
147A ASN 5.2 2.3 - - - +
148A ASP 3.8 3.4 - - - -
149A THR* 3.0 31.0 + - - +
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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