Contacts of the strand formed by residues 223 - 227 (chain A) in PDB entry 1HUP
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 VAL 223 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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119A PHE* 4.6 3.4 - - + -
120A LEU 3.5 11.9 - - - +
121A THR* 4.0 10.3 - - - +
131A VAL* 4.3 3.6 - - - +
135A CYS* 3.8 1.4 - - - -
142A VAL* 3.5 11.4 - - - +
143A ALA* 2.9 41.3 + - + +
154A ILE* 4.5 9.0 - - + -
157A LEU* 4.3 16.2 - - + -
158A ILE* 3.8 15.7 - - + -
162A ALA* 3.7 28.5 - - + -
163A PHE 4.9 4.3 + - - +
221A LEU* 3.7 3.6 + - + -
222A ALA* 1.3 81.0 - - - +
224A CYS* 1.3 67.6 + - - +
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Residues in contact with CYS 224 (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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118A PHE 3.6 1.2 - - - +
119A PHE* 3.4 2.6 - - - -
120A LEU 2.9 33.9 + - - +
131A VAL* 5.1 0.2 - - - -
134A LEU* 4.7 13.5 - - - -
135A CYS* 2.0 54.1 - - + -
138A PHE* 6.0 0.4 - - - -
140A ALA* 3.8 4.0 - - + -
141A SER 3.2 7.9 - - - +
143A ALA* 4.3 1.6 - - - -
222A ALA 5.3 0.7 - - - -
223A VAL* 1.3 77.3 - - - +
225A GLU* 1.3 59.7 + - - +
226A PHE* 3.6 24.3 - - + -
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Residues in contact with GLU 225 (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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117A LYS* 2.8 46.7 + - + +
118A PHE 3.5 4.7 - - - +
119A PHE* 3.6 21.5 - - + -
140A ALA* 3.3 2.8 - - - +
141A SER* 2.8 48.5 + - - +
142A VAL 3.6 14.2 - - - +
143A ALA* 3.9 1.7 - - - +
144A THR* 3.0 17.4 + - - +
146A ARG* 3.7 12.1 + - - -
224A CYS* 1.3 73.4 - - - +
226A PHE* 1.3 61.6 + - - +
227A PRO* 4.3 1.6 - - - +
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Residues in contact with PHE 226 (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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117A LYS* 3.5 5.0 - - - -
118A PHE* 2.8 52.0 + - + +
120A LEU* 3.7 33.4 - - + -
138A PHE* 3.7 44.9 - + + -
140A ALA* 3.8 14.6 - - + -
224A CYS* 3.6 25.8 - - + -
225A GLU* 1.3 77.9 - - - +
227A PRO* 1.3 74.2 - - + +
228A ILE 3.4 0.5 + - - -
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Residues in contact with PRO 227 (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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116A ASN 3.7 7.4 - - - +
117A LYS* 6.1 0.2 - - + -
139A GLN* 3.9 22.9 - - + +
140A ALA* 4.8 0.4 - - - -
225A GLU 4.4 2.0 - - - +
226A PHE* 1.3 91.4 - - + +
228A ILE* 1.3 58.6 + - - +
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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