Contacts of the strand formed by residues 224 - 228 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47B MET* 5.4 0.2 - - - -
219B GLN* 4.0 0.2 - - - +
220B PRO* 4.4 3.4 - - - -
221B MET* 2.9 38.9 + - + +
223B LEU* 1.3 80.1 - - - +
225B GLY* 1.3 70.7 + - - +
226B HIS* 3.8 19.3 - - + -
271B SER 4.2 4.7 - - - +
274B LEU* 4.0 17.7 - - + -
275B ASP* 3.0 32.7 + - + +
278B LEU* 4.0 22.4 - - + -
332B LEU* 3.5 38.1 - - + -
333B VAL 3.4 8.3 - - - +
334B PHE* 4.3 4.0 - - + -
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Residues in contact with GLY 225 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3B VAL* 4.1 14.1 - - - +
202B VAL* 4.7 4.1 - - - +
204B HIS* 4.2 9.4 - - - -
219B GLN* 3.5 5.6 - - - -
220B PRO* 4.4 12.3 - - - +
224B LEU* 1.3 74.7 - - - +
226B HIS* 1.3 59.2 + - - -
331B LEU 3.7 1.6 - - - +
332B LEU* 3.6 4.0 - - - -
333B VAL* 2.7 37.9 + - - -
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Residues in contact with HIS 226 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1B CYS* 4.5 3.5 - - - +
204B HIS* 3.0 21.3 + - - -
219B GLN* 2.7 21.1 + - - +
224B LEU* 3.8 17.5 - - + -
225B GLY* 1.3 72.6 - - - -
227B ASN* 1.3 70.3 + - - +
228B GLY* 3.7 33.4 + - - -
229B GLU 4.0 3.2 + - - -
230B ILE* 4.3 13.1 - - + +
270B ASP* 4.1 14.6 - - - -
271B SER* 2.9 29.7 + - - +
274B LEU* 4.1 10.3 - - + +
329B PRO 4.1 5.3 + - - -
330B ALA* 4.1 5.4 - - + +
331B LEU 3.7 1.3 - - - -
332B LEU* 3.6 22.2 - - + -
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Residues in contact with ASN 227 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1B CYS* 3.4 36.9 + - + +
3B VAL* 4.0 21.9 - - + +
31B ARG* 4.7 1.2 + - - -
225B GLY 4.3 0.2 - - - -
226B HIS* 1.3 74.8 - - - +
228B GLY* 1.3 64.2 + - - +
330B ALA* 3.3 3.8 - - - -
331B LEU* 2.8 40.4 + - + +
350B ARG* 2.8 34.2 + - - +
351B PRO* 5.0 1.0 - - - +
366B SER* 4.4 6.4 + - - -
1011B SER* 5.2 1.2 - - - -
1013B GLU* 2.9 22.5 + - - +
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Residues in contact with GLY 228 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1B CYS* 5.4 3.2 - - - -
226B HIS* 3.7 16.2 + - - -
227B ASN* 1.3 83.5 - - - +
229B GLU* 1.3 74.8 + - - +
270B ASP* 4.1 1.2 - - - +
271B SER* 5.4 0.3 + - - -
329B PRO* 3.3 18.2 - - - -
350B ARG* 4.5 4.0 - - - -
1011B SER* 6.1 2.5 - - - -
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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