Contacts of the strand formed by residues 299 - 304 (chain A) in PDB entry 1QFM
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 299 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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295A ASN* 3.2 3.1 - - - -
296A GLU* 2.9 43.0 + - + +
297A GLY 3.3 0.2 - - - -
298A THR* 1.3 78.3 - - - +
300A PHE* 1.3 61.5 + - - +
301A THR* 4.0 2.6 + - - +
315A ASN* 3.8 33.9 - - + +
316A ILE 3.8 5.6 - - - +
317A ASP* 3.7 24.7 - - + +
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Residues in contact with PHE 300 (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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241A SER* 4.3 2.9 - - - -
246A TYR* 3.4 30.7 - + - -
248A LEU* 3.9 14.6 - - + -
292A TYR* 3.5 37.5 - + - -
294A THR 3.7 2.0 - - - -
295A ASN* 3.6 13.7 - - + -
297A GLY 3.5 19.1 - - - -
298A THR 3.5 11.4 - - - -
299A VAL* 1.3 72.0 - - - +
301A THR* 1.3 61.0 + - - +
302A PHE* 3.5 26.0 - + + -
314A ILE 3.6 0.5 - - - +
315A ASN* 3.2 4.5 - - - -
316A ILE 2.8 41.3 + - - +
318A PHE* 3.3 39.7 - + + -
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Residues in contact with THR 301 (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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292A TYR* 3.9 1.9 - - - -
293A VAL* 2.9 40.7 + - + +
294A THR* 2.8 27.8 + - - +
295A ASN* 5.3 0.2 - - - -
299A VAL* 4.0 3.7 + - - +
300A PHE* 1.3 72.2 - - - +
302A PHE* 1.3 63.5 + - - +
313A LEU* 4.3 15.3 - - + -
314A ILE 3.3 6.3 - - - +
315A ASN* 2.7 23.6 + - - +
329A LEU* 4.0 16.2 - - + -
349A LEU* 5.1 0.9 - - + -
366A LEU* 3.9 18.0 - - + +
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Residues in contact with PHE 302 (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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248A LEU* 4.9 1.8 - - + -
261A LEU* 4.0 38.4 - - + -
282A LEU* 4.6 8.1 - - + -
290A TYR* 3.9 18.8 - + + -
291A ASP 3.2 23.1 - - - +
292A TYR* 3.6 20.2 - + + -
293A VAL* 4.3 0.2 - - - -
300A PHE* 3.5 42.6 - + + -
301A THR* 1.3 73.4 - - - +
303A LYS* 1.3 67.5 + - - +
313A LEU* 3.4 8.3 - - - -
314A ILE* 2.9 42.6 + - + +
316A ILE* 3.9 31.4 - - + -
318A PHE* 4.7 0.9 - + - -
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Residues in contact with LYS 303 (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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289A GLU* 3.6 2.3 - - - +
290A TYR* 3.5 2.8 - - - -
291A ASP* 2.8 64.5 + - + +
293A VAL* 3.9 6.6 - - + +
302A PHE* 1.3 72.9 - - - +
304A THR* 1.3 62.1 + - - +
311A TYR* 3.5 34.7 - - + -
312A ARG 3.4 9.6 - - - +
313A LEU* 3.7 11.3 - - + +
338A LEU* 3.7 29.5 + - + +
339A GLU 3.4 22.8 + - - +
340A TRP* 4.0 15.0 - - - +
341A VAL* 4.3 5.4 - - + +
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Residues in contact with THR 304 (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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289A GLU* 2.7 20.6 + - - -
290A TYR* 3.4 14.2 - - - -
302A PHE 5.0 0.2 - - - -
303A LYS* 1.3 75.1 - - - +
305A ASN* 1.3 64.9 + - - +
306A ARG* 2.9 25.8 + - + +
308A SER* 3.5 2.3 + - - +
311A TYR* 3.2 10.1 - - - -
312A ARG* 2.9 54.4 + - + +
314A ILE* 3.8 29.4 - - + -
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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