Contacts of the strand formed by residues 291 - 298 (chain A) in PDB entry 1F0C
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 PHE 291 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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250A MET* 5.5 3.8 - - + -
288A ILE* 5.0 3.1 - - + -
289A PRO* 3.4 18.2 - - + -
290A LYS* 1.3 76.0 - - - +
292A LYS* 1.3 65.9 + - - +
293A VAL* 3.9 16.8 - - + -
338A ILE* 4.0 13.5 - - + -
339A ASP* 3.4 2.1 - - - -
340A VAL* 2.8 65.5 + - + +
370B PHE* 4.3 12.1 - + - -
372B TYR* 3.4 48.5 - + - -
388B TYR* 3.6 36.6 - + + +
391B PRO* 6.1 1.3 - - + -
392B THR 6.4 0.2 - - - +
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Residues in contact with LYS 292 (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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291A PHE* 1.3 79.2 - - - +
293A VAL* 1.3 71.4 + - - +
337A TYR* 3.2 34.1 - - + +
338A ILE 3.3 2.7 - - - +
339A ASP* 3.8 29.6 + - + +
392B THR* 4.1 16.8 + - - +
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Residues in contact with VAL 293 (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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49A ASN* 4.4 28.7 - - + +
50A VAL 5.7 0.2 - - - -
51A PHE* 4.8 14.9 - - + +
291A PHE* 3.9 21.8 - - + -
292A LYS* 1.3 85.6 - - - +
294A THR* 1.3 79.3 + - - +
295A GLY* 4.8 1.3 - - - +
297A TYR* 5.7 1.1 - - - +
336A THR* 5.8 0.2 - - - -
337A TYR* 3.3 3.7 - - - -
338A ILE* 2.9 43.5 + - + +
372B TYR* 4.9 3.6 - - - +
388B TYR* 5.5 3.6 - - + -
390B SER 5.7 0.4 - - - +
392B THR* 4.5 14.6 - - - +
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Residues in contact with THR 294 (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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168A LYS 5.5 2.0 - - - +
293A VAL* 1.3 86.6 - - - +
295A GLY* 1.3 60.0 + - - +
336A THR* 3.1 10.1 - - - +
337A TYR* 3.6 29.6 - - + -
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Residues in contact with GLY 295 (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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293A VAL* 4.8 1.3 - - - +
294A THR* 1.3 77.3 - - - +
296A SER* 1.3 62.3 + - - -
297A TYR* 3.9 21.3 - - - -
335A LYS* 3.2 5.4 - - - +
336A THR* 2.9 40.9 + - - +
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Residues in contact with SER 296 (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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45A MET* 5.8 1.4 - - - +
295A GLY* 1.3 74.8 - - - -
297A TYR* 1.3 67.8 + - - +
333A ILE* 3.8 8.3 - - - +
334A HIS 3.5 4.0 - - - -
335A LYS* 3.4 30.1 - - - +
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Residues in contact with TYR 297 (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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41A ILE* 3.7 28.5 - - + -
45A MET* 3.8 32.3 - - + -
49A ASN 4.1 2.1 + - - -
50A VAL* 3.4 10.3 - - + -
51A PHE* 2.8 46.8 + - - +
52A ILE* 4.0 9.0 - - + -
293A VAL* 5.7 1.6 - - - +
295A GLY* 3.9 26.3 - - - -
296A SER* 1.3 78.0 + - - +
298A ASN* 1.3 61.0 + - - +
299A LEU* 3.8 18.0 + - + -
333A ILE* 2.9 23.2 - - - +
334A HIS* 2.8 41.5 + + + +
336A THR* 3.9 3.5 + - + -
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Residues in contact with ASN 298 (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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41A ILE* 6.0 0.7 - - - +
297A TYR* 1.3 72.4 - - - +
299A LEU* 1.3 59.9 + - - +
300A VAL* 3.1 32.7 + - - +
301A ASP* 4.7 8.4 + - - +
302A ALA* 5.1 4.2 + - - +
331A ALA* 6.1 2.6 - - - +
332A MET 3.7 8.9 + - - +
333A ILE* 4.4 6.3 - - + -
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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