Contacts of the strand formed by residues 90 - 95 (chain A) in PDB entry 1IPC
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 ASP 90 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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46A TRP 4.4 0.2 - - - -
47A PHE* 3.5 12.4 - - - -
48A PHE* 3.0 54.9 + - + +
56A TRP* 4.9 9.0 + - - -
85A LEU* 4.9 3.4 - - - -
89A CYS* 1.3 77.6 - - - +
91A TYR* 1.3 67.5 + - - +
92A SER* 4.6 3.8 - - - +
153A VAL* 4.3 6.8 - - + +
154A VAL* 3.2 11.0 - - - +
155A ASN* 3.0 22.0 + - - +
156A VAL* 5.5 0.4 - - - -
157A ARG* 2.8 38.6 + - - -
1000A MGP 4.7 2.1 + - - -
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Residues in contact with TYR 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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45A LEU* 4.6 9.2 - - + -
46A TRP 3.3 11.7 - - - -
47A PHE* 3.9 17.3 - + - -
63A ILE* 4.1 17.3 - - + -
79A ILE* 3.5 30.8 - - + +
80A GLN* 2.8 33.8 + - - -
82A SER* 3.6 22.9 - - - -
85A LEU* 3.8 26.8 - - + +
90A ASP* 1.3 77.7 - - - +
92A SER* 1.3 65.3 + - - +
130A TRP* 3.9 18.3 - + + -
153A VAL* 3.5 1.0 - - - +
154A VAL* 3.0 42.9 + - + +
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Residues in contact with SER 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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44A ALA 3.4 2.3 - - - +
45A LEU* 3.3 7.2 - - - +
46A TRP* 2.7 42.9 + - - +
60A LEU* 5.2 3.8 - - - +
90A ASP* 4.6 4.3 - - - +
91A TYR* 1.3 78.9 + - - +
93A LEU* 1.3 59.6 + - - +
94A PHE* 4.0 1.6 - - - -
100A PRO* 3.7 32.6 + - - +
130A TRP* 4.5 0.2 - - - -
152A ALA 3.3 11.0 - - - -
153A VAL* 3.5 18.3 - - - +
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Residues in contact with LEU 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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43A TRP* 4.0 13.7 - - + -
44A ALA 3.4 16.2 - - - +
45A LEU* 4.0 14.8 - - + +
66A PHE* 3.7 29.4 - - + -
72A PHE* 5.5 0.9 - - + -
92A SER* 1.3 71.9 - - - +
94A PHE* 1.3 60.8 + - - +
130A TRP* 4.4 2.3 - - + -
134A LEU* 3.7 31.9 - - + +
137A LEU* 3.6 22.9 - - + +
138A ILE* 3.9 27.4 - - + -
151A GLY* 3.1 4.2 - - - -
152A ALA 2.9 31.1 + - - +
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Residues in contact with PHE 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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43A TRP* 3.6 4.5 - - - -
44A ALA* 2.9 32.7 + - - +
46A TRP* 4.7 5.8 - + - +
92A SER* 4.0 1.1 - - - -
93A LEU* 1.3 87.2 - - - +
95A LYS* 1.3 66.8 + - - +
98A ILE* 3.3 36.6 - - + +
100A PRO* 3.6 26.9 - - + -
107A ASN* 4.0 11.0 - - - -
150A CYS* 3.5 22.0 - - + -
151A GLY* 4.0 1.6 - - - -
152A ALA 3.5 12.1 - - - -
153A VAL* 3.5 25.4 - - + -
166A TRP* 3.6 44.0 - + + -
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Residues in contact with LYS 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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41A ASN* 3.3 39.4 - - - +
42A ARG 3.8 3.4 - - - +
43A TRP* 3.2 35.1 - - + -
44A ALA* 5.4 0.5 - - - +
94A PHE* 1.3 73.3 - - - +
96A ASP* 1.3 67.8 + - - +
98A ILE* 2.9 41.5 + - + +
106A LYS* 6.0 2.6 - - - +
140A GLU* 5.2 1.3 - - - +
146A SER 4.3 10.3 - - - -
147A ASP* 5.1 6.6 + - - +
149A VAL* 3.0 27.5 + - - -
150A CYS* 3.0 16.7 + - - +
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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