Contacts of the strand formed by residues 290 - 294 (chain C) in PDB entry 1IR1
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 290 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153C HIS* 3.8 19.3 - - + +
158C GLU* 3.9 50.7 - - + +
161C LYS* 5.5 8.5 - - + -
162C LEU* 4.1 25.4 - - + -
199C PHE* 5.5 0.9 - - + -
263C PRO* 2.9 22.8 + - + +
264C ILE* 3.7 21.1 - - + -
265C VAL* 3.1 28.9 + - - +
288C GLY 5.4 1.6 - - - +
289C LEU* 1.3 75.2 - - - +
291C LEU* 1.3 59.6 + - - +
324C ASP* 3.3 15.0 - - + +
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Residues in contact with LEU 291 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152C PRO* 4.2 8.3 - - + -
264C ILE* 4.8 1.8 - - - -
265C VAL* 3.5 15.5 - - + +
267C HIS* 4.2 4.3 - - + +
277C ASN* 4.7 3.6 - - - +
280C LEU* 3.8 26.5 - - + -
281C SER* 3.9 27.6 - - - +
284C CYS* 4.1 10.1 - - - -
290C LEU* 1.3 74.4 - - - +
292C HIS* 1.3 65.0 + - - +
293C ILE* 3.7 21.8 + - + -
322C GLY 3.7 23.6 - - - +
323C GLY* 3.8 2.6 - - - -
324C ASP* 2.8 46.0 + - - +
325C HIS* 3.3 4.4 + - - -
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Residues in contact with HIS 292 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201C KCX 3.8 7.2 - - - -
239C TYR* 3.3 40.5 - + + -
264C ILE* 4.0 7.3 - - + +
265C VAL 2.9 15.0 + - - +
266C MET* 3.1 15.1 - - + +
267C HIS 3.0 25.8 + - - -
290C LEU 4.2 0.4 - - - -
291C LEU* 1.3 72.4 - - - +
293C ILE* 1.3 68.0 + - - +
294C HIS* 4.3 1.9 + - - -
325C HIS* 3.1 35.2 + - + +
327C HIS* 2.9 40.8 + + - -
377C VAL* 3.9 16.4 - - + -
401C GLN* 3.9 3.1 - - - -
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Residues in contact with ILE 293 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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267C HIS* 3.5 7.9 - - + +
269C TYR* 3.2 42.2 - - + -
277C ASN* 3.4 25.4 - - - +
291C LEU* 3.7 25.6 - - + -
292C HIS* 1.3 80.7 + - - +
294C HIS* 1.3 59.5 - - - +
318C LEU* 3.8 13.7 - - + -
322C GLY 4.2 2.0 - - - +
323C GLY* 3.8 20.2 - - - -
325C HIS 3.0 20.0 + - - +
326C ILE* 3.4 22.2 - - + +
327C HIS* 3.5 12.3 + - - -
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Residues in contact with HIS 294 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201C KCX 3.3 27.8 - - - -
204C GLU* 3.1 32.1 + - + +
266C MET* 3.9 10.3 - - + -
267C HIS 3.0 6.4 + - - +
268C ASP* 3.4 33.2 + - - +
269C TYR* 3.5 10.2 + - - -
270C LEU 4.7 0.2 + - - -
292C HIS* 4.0 1.9 + - - +
293C ILE* 1.3 74.8 - - - +
295C ARG* 1.3 59.8 + - - +
296C ALA* 3.0 40.9 + - + +
327C HIS* 3.8 16.2 - + - +
501C CAP 2.9 35.5 + - - -
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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