Contacts of the strand formed by residues 224 - 228 (chain A) in PDB entry 1OFD
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 LEU 224 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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47A MET* 5.4 0.2 - - - -
219A GLN* 5.6 0.2 - - - +
220A PRO* 4.5 3.1 - - - -
221A MET* 2.9 34.1 + - + +
222A ARG 3.9 0.2 - - - -
223A LEU* 1.3 79.5 - - - +
225A GLY* 1.3 83.2 + - - +
226A HIS* 3.9 15.3 - - + -
271A SER 4.3 4.5 - - - +
274A LEU* 4.0 15.7 - - + -
275A ASP* 2.9 33.7 + - + +
278A LEU* 3.9 25.1 - - + -
332A LEU* 3.6 31.6 - - + -
333A VAL 3.4 7.4 - - - +
334A PHE* 4.3 3.6 - - + -
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Residues in contact with GLY 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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3A VAL* 4.1 14.9 - - - +
202A VAL* 4.7 3.9 - - - +
204A HIS* 4.2 9.6 - - - -
219A GLN* 3.6 5.2 - - - -
220A PRO* 4.4 12.3 - - - +
224A LEU* 1.3 76.2 - - - +
226A HIS* 1.3 60.4 + - - -
331A LEU 3.7 1.4 - - - +
332A LEU* 3.6 1.7 - - - -
333A VAL* 2.7 39.3 + - - -
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Residues in contact with HIS 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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1A CYS* 4.5 4.2 - - - +
204A HIS* 3.0 22.0 + - - -
219A GLN* 2.8 20.4 + - - +
224A LEU* 3.9 16.6 - - + -
225A GLY* 1.3 73.5 - - - +
227A ASN* 1.3 67.5 + - - +
228A GLY* 3.6 34.4 + - - -
229A GLU 4.0 2.3 + - - -
230A ILE* 4.3 11.8 - - + +
270A ASP* 3.7 17.0 - - - -
271A SER* 2.8 30.1 + - - +
274A LEU* 4.1 10.3 - - + +
329A PRO 4.2 4.4 + - - -
330A ALA* 4.2 4.3 - - + +
331A LEU 3.7 1.3 - - - -
332A LEU* 3.5 24.2 - - + -
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Residues in contact with ASN 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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1A CYS* 3.5 36.1 + - + +
3A VAL* 4.0 21.7 - - + +
31A ARG* 4.8 1.2 + - - -
225A GLY 4.2 0.4 - - - -
226A HIS* 1.3 74.8 - - - +
228A GLY* 1.3 63.6 + - - +
330A ALA* 3.2 4.2 - - - -
331A LEU* 2.8 39.8 + - + +
350A ARG* 2.8 36.3 + - + +
351A PRO* 5.0 1.0 - - - +
366A SER* 4.5 6.9 + - - -
1011A SER* 5.2 1.0 - - - -
1013A GLU* 2.9 22.5 + - - +
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Residues in contact with GLY 228 (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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1A CYS* 5.6 1.7 - - - -
226A HIS* 3.6 17.0 + - - -
227A ASN* 1.3 84.9 - - - +
229A GLU* 1.3 73.7 + - - +
270A ASP* 4.0 0.7 - - - +
329A PRO* 3.1 19.5 - - - -
350A ARG* 4.4 3.6 - - - -
503A THR 5.4 0.2 - - - -
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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