Contacts of the strand formed by residues 263 - 268 (chain A) in PDB entry 4HYY
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 ALA 263 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99A PHE* 4.4 1.6 - - + -
101A ILE* 4.2 10.8 - - + -
116A ILE* 3.9 20.4 - - + +
117A GLU 3.6 28.5 - - - +
118A SER* 3.8 4.9 + - - +
218A LYS 2.9 14.1 + - - +
219A LEU* 3.3 9.4 - - + +
220A LEU 3.0 23.4 + - - -
262A VAL* 1.3 75.8 - - - +
264A VAL* 1.3 61.1 + - - +
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Residues in contact with VAL 264 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116A ILE* 4.7 1.3 - - - +
117A GLU 5.2 0.2 - - - +
120A ALA 3.1 9.7 + - - +
121A ILE* 3.3 21.6 - - + -
122A THR* 2.8 28.1 + - - -
220A LEU* 3.3 20.2 - - + +
222A ILE* 4.8 0.2 - - + -
253A LEU* 4.2 24.5 - - + +
256A ILE* 5.1 0.2 - - + -
257A SER* 3.7 34.8 - - - +
262A VAL* 4.1 6.1 - - + -
263A ALA* 1.3 77.9 - - - +
265A PHE* 1.3 61.7 + - - +
266A VAL* 3.9 21.1 - - + -
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Residues in contact with PHE 265 (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 ILE* 4.1 22.0 - - + -
122A THR* 3.4 13.2 - - + -
124A ALA* 3.9 20.2 - - + -
132A LYS 4.3 0.7 - - - -
135A LEU* 3.6 36.3 - - + -
136A SER* 3.4 24.9 - - - -
139A LEU* 3.7 22.9 - - + -
219A LEU* 4.0 19.3 - - + -
220A LEU 2.8 8.1 + - - +
221A ILE* 3.2 18.1 - - + +
222A ILE 3.1 23.0 + - - -
264A VAL* 1.3 73.6 - - - +
266A VAL* 1.3 64.8 + - - +
267A THR* 4.0 20.0 - - + -
301A ILE* 5.7 0.4 - - + -
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Residues in contact with VAL 266 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A ILE* 4.3 11.2 - - + -
122A THR 2.9 14.8 + - - +
123A GLU* 3.3 16.8 - - + -
124A ALA* 2.8 27.0 + - - +
222A ILE* 3.2 32.5 - - + +
225A ILE* 3.8 32.1 - - + -
250A LEU* 6.3 0.4 - - + -
253A LEU* 4.7 0.9 - - + -
264A VAL* 3.9 19.5 - - + -
265A PHE* 1.3 83.8 - - - +
267A THR* 1.3 65.0 + - - +
293A LEU* 5.4 2.0 - - + -
297A SER* 5.2 1.3 - - - +
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Residues in contact with THR 267 (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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124A ALA 3.1 8.1 - - - +
132A LYS* 3.8 29.8 - - + +
136A SER* 3.7 20.4 - - - +
222A ILE 3.2 4.2 + - - +
223A ASP* 2.5 33.2 + - + +
224A SER* 3.0 15.7 - - - -
225A ILE* 2.9 31.9 + - - +
265A PHE* 4.0 11.7 - - + -
266A VAL* 1.3 76.0 - - - +
268A ASN* 1.3 60.8 + - - +
269A GLN* 4.9 0.2 + - - -
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Residues in contact with ASN 268 (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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123A GLU* 3.2 28.7 - - - +
124A ALA 3.0 5.3 + - - -
125A PHE* 3.2 24.5 - - + +
126A GLY 3.8 0.9 + - - -
132A LYS* 3.6 11.6 - - - +
225A ILE* 3.6 20.0 - - + +
226A MET* 3.9 6.9 - - - +
267A THR* 1.3 80.0 - - - +
269A GLN* 1.3 82.4 + - - +
287A PRO* 4.1 2.1 - - - +
288A ILE* 3.1 48.0 + - - +
293A LEU* 3.5 4.1 - - - +
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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