Contacts of the strand formed by residues 302 - 306 (chain B) in PDB entry 5FS9
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 SER 302 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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300B VAL* 3.6 1.3 - - - +
301B LYS* 1.3 81.0 - - - +
303B ILE* 1.3 64.2 + - - +
329B GLU* 2.7 33.9 + - - +
331B ILE* 4.0 5.4 - - - +
378B LYS* 4.8 5.8 - - - -
390B GLU 4.8 0.7 - - - -
391B THR* 2.8 27.8 + - - -
392B ASP* 2.9 44.0 + - - +
393B HIS 3.4 2.3 + - - -
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Residues in contact with ILE 303 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293B LEU* 4.4 8.7 - - + -
296B ILE* 4.2 6.1 - - + -
297B SER* 3.8 36.3 - - - +
300B VAL* 3.7 15.0 - - + -
301B LYS 5.8 0.2 - - - -
302B SER* 1.3 79.8 + - - +
304B THR* 1.3 67.7 + - - +
305B ILE 4.9 0.2 - - - +
319B LEU* 4.0 23.3 - - + -
329B GLU 3.1 8.2 + - - +
330B VAL* 3.4 9.2 - - + +
331B ILE* 2.9 25.1 + - - +
391B THR* 3.7 0.2 - - - -
393B HIS* 3.5 14.8 - - + +
395B VAL* 3.8 28.0 - - + -
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Residues in contact with THR 304 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303B ILE* 1.3 72.9 - - - +
305B ILE* 1.3 71.8 + - - +
306B ILE* 3.9 4.8 + - + -
331B ILE* 3.3 25.3 - - + +
333B LEU* 3.9 30.1 - - + -
381B ILE* 4.1 10.8 - - + -
389B VAL* 4.3 1.8 - - + +
391B THR* 2.9 33.8 + - - +
393B HIS 2.9 8.2 + - - -
394B ILE* 3.3 5.3 - - - +
395B VAL 2.8 26.2 + - - +
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Residues in contact with ILE 305 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303B ILE* 4.9 0.2 - - + -
304B THR* 1.3 77.5 - - - +
306B ILE* 1.3 64.1 + - - +
307B GLY 3.9 8.7 + - - +
312B GLY* 3.7 28.3 - - - +
315B LEU* 3.7 10.5 - - + -
316B ALA* 3.2 44.0 - - + +
319B LEU* 4.0 21.1 - - + -
330B VAL* 4.0 11.0 - - + -
331B ILE 2.7 11.7 + - - +
332B GLN* 3.3 5.1 - - + -
333B LEU 2.9 26.3 + - - +
395B VAL* 3.3 18.4 - - + +
397B ALA* 4.8 4.0 - - + -
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Residues in contact with ILE 306 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267B LEU* 3.9 33.2 - - + -
270B ILE* 4.3 8.1 - - + -
304B THR* 4.3 5.4 - - + -
305B ILE* 1.3 75.5 - - - +
307B GLY* 1.3 59.3 + - - +
333B LEU* 3.5 29.2 - - + +
334B PHE* 5.6 1.6 - - - -
335B PRO* 6.1 2.2 - - + -
369B VAL* 4.5 11.4 - - + -
372B VAL* 5.7 0.9 - - + -
381B ILE* 4.8 4.9 - - + -
394B ILE* 3.5 36.1 - - + -
395B VAL 2.8 11.8 + - - +
396B ALA* 4.6 5.2 - - + -
397B ALA* 2.9 28.6 + - - +
398B VAL* 3.5 14.4 - - + +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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