Contacts of the strand formed by residues 296 - 301 (chain A) in PDB entry 1FBA
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 ALA 296 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23A VAL* 3.7 45.5 - - + +
265A THR 3.8 6.9 + - - +
266A GLY* 4.4 0.2 - - - -
267A VAL* 2.9 29.0 + - - +
295A TRP* 1.3 75.7 - - - +
297A LEU* 1.3 59.9 + - - +
298A THR* 3.9 4.0 - - + -
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Residues in contact with LEU 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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253A VAL* 4.7 2.7 - - + -
256A LEU* 4.0 8.1 - - + -
267A VAL* 3.7 17.9 - - + -
269A PHE* 3.7 26.2 - - + -
283A LEU* 3.7 4.9 - - - +
286A ILE* 3.9 16.8 - - + -
287A ASN* 2.8 45.8 + - - +
293A ARG* 3.4 44.9 - - + +
295A TRP* 3.4 25.7 + - + +
296A ALA* 1.3 69.4 - - - +
298A THR* 1.3 61.8 + - - +
338A ALA* 3.7 8.4 + - - +
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Residues in contact with THR 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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22A ILE 5.1 0.2 - - - +
23A VAL* 3.8 21.3 - - + -
27A LYS 2.7 28.7 + - - +
28A GLY* 3.6 2.1 - - - -
267A VAL 2.8 12.4 + - - +
268A THR* 3.7 24.5 - - + -
269A PHE* 2.9 32.5 + - - +
283A LEU* 3.7 8.1 - - - +
296A ALA* 5.1 2.2 - - + -
297A LEU* 1.3 77.4 - - - +
299A PHE* 1.3 80.7 + - - +
338A ALA* 3.5 12.5 - - - +
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Residues in contact with PHE 299 (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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27A LYS 4.1 2.9 - - - -
28A GLY* 3.4 38.2 - - - -
29A ILE* 2.8 41.9 + - - +
72A ASN 3.5 11.2 - - - -
73A ILE* 3.8 16.4 - - + -
268A THR* 3.9 8.3 - - - +
269A PHE 3.8 3.4 - - - -
283A LEU* 3.8 6.5 - - + -
298A THR* 1.3 91.2 + - - +
300A SER* 1.3 59.7 + - - +
301A TYR* 3.6 32.1 - + + -
305A LEU* 3.9 13.0 - - + -
331A ALA* 4.4 3.8 - - - -
334A ASN* 3.5 44.9 - - + -
335A GLY* 3.7 5.4 - - - -
338A ALA* 4.7 0.2 - - + -
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Residues in contact with SER 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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29A ILE* 3.4 30.3 - - - +
31A ALA* 4.5 1.6 - - - +
77A ILE* 3.8 6.1 - - - +
185A ILE* 5.1 0.3 - - - +
229A LYS* 3.1 42.7 + - - +
268A THR* 3.7 23.6 - - - -
269A PHE 2.9 15.6 + - - +
270A LEU* 3.9 3.6 - - - -
271A SER 4.8 0.2 + - - -
299A PHE* 1.3 75.0 - - - +
301A TYR* 1.3 62.2 + - - +
302A GLY 4.2 0.3 + - - -
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Residues in contact with TYR 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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29A ILE 3.1 6.9 + - - +
30A LEU* 3.6 7.3 - - - +
31A ALA* 2.8 24.7 + - - -
232A MET* 3.4 16.3 - - + +
269A PHE* 3.2 30.4 - - + +
270A LEU 4.0 1.6 - - - -
271A SER* 3.9 21.5 - - - -
279A ALA* 2.8 36.1 + - + +
283A LEU* 3.7 8.9 - - + +
299A PHE* 3.6 21.9 - + + -
300A SER* 1.3 77.1 - - - +
302A GLY* 1.3 61.7 + - - +
304A ALA* 4.0 21.1 - - + -
305A LEU* 3.7 20.6 - - + +
334A ASN* 3.5 35.7 - - - -
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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