Contacts of the strand formed by residues 217 - 221 (chain A) in PDB entry 4OHN
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 217 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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130A VAL* 3.9 13.9 - - + -
131A THR 3.3 22.0 - - - +
132A LYS* 3.8 21.7 - - + -
133A LYS* 3.0 23.1 + - - +
189A LEU* 3.7 26.9 - - + -
190A LYS* 3.5 18.0 - - - +
208A LEU* 3.6 23.1 - - + -
213A VAL* 3.4 21.5 - - + +
214A LEU* 3.2 11.9 + - - +
215A ASN 3.5 1.0 - - - -
216A ASP* 1.3 94.7 - - + +
218A ASN* 1.3 58.7 + - - +
219A VAL* 4.2 3.3 + - - +
302A ACT 2.6 42.3 + - + +
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Residues in contact with ASN 218 (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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129A LEU 3.6 0.7 - - - +
130A VAL* 3.2 7.6 - - - +
131A THR* 2.8 42.4 + - - +
132A LYS 3.9 1.6 + - - -
133A LYS* 3.1 44.7 + - - +
136A GLY* 4.8 1.2 - - - -
137A ILE 3.3 24.6 + - - +
138A THR* 3.6 18.9 - - + +
217A TYR* 1.3 73.5 - - - +
219A VAL* 1.3 62.3 + - - +
220A PHE* 4.1 10.8 - - + -
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Residues in contact with VAL 219 (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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128A VAL* 3.7 29.8 - - + -
129A LEU 3.5 2.9 - - - -
130A VAL* 4.1 7.2 - - + -
201A ARG* 4.6 15.1 + - + +
204A ALA* 4.3 10.8 - - + -
205A ASN* 4.4 13.7 - - - +
208A LEU* 3.6 31.6 - - + -
214A LEU* 4.9 8.3 - - + -
217A TYR 4.2 4.5 + - - +
218A ASN* 1.3 80.3 - - - +
220A PHE* 1.3 63.0 + - - +
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Residues in contact with PHE 220 (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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128A VAL* 3.8 7.2 - - - +
129A LEU* 2.8 76.6 + - + +
131A THR* 3.9 10.5 - - + -
137A ILE* 3.5 24.2 - - + -
138A THR* 3.5 38.8 - - - +
139A THR* 3.5 14.6 - - - -
201A ARG* 5.2 3.4 - - - +
218A ASN* 4.1 6.1 - - + -
219A VAL* 1.3 84.9 - - - +
221A THR* 1.3 75.5 + - - +
222A VAL* 3.8 7.2 - - + -
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Residues in contact with THR 221 (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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126A GLU* 4.0 15.3 - - + -
127A GLN 3.8 12.1 - - - +
128A VAL* 3.6 14.1 - - + +
201A ARG* 3.4 28.4 + - - +
220A PHE* 1.3 85.0 - - - +
222A VAL* 1.3 63.6 + - - +
223A GLY 3.7 5.7 + - - -
224A LEU 5.9 1.6 - - - -
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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