Contacts of the strand formed by residues 248 - 253 (chain B) in PDB entry 4F5G
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 248 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12A PHE* 3.9 2.8 - - - -
93B PHE* 4.6 6.5 - - + -
217B LEU* 3.9 3.5 - - - +
218B PRO* 3.5 36.6 - - + -
220B ILE* 5.4 4.7 - - + -
238B LEU* 4.5 4.3 - - + +
241B PHE* 4.1 13.2 - - + -
242B ALA* 3.5 39.0 - - + +
245B HIS* 4.0 12.1 - - + +
247B GLU* 1.3 82.1 - - - +
249B ILE* 1.3 72.8 + - - +
250B VAL* 5.0 5.8 - - + -
269B THR 4.5 0.2 - - - -
270B LEU* 3.7 0.9 - - - -
271B VAL* 3.0 51.7 + - + +
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Residues in contact with ILE 249 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12A PHE* 3.9 9.4 - - + -
120B ALA* 4.0 11.4 - - + -
123B PHE* 4.6 1.8 - - + -
124B LEU* 3.8 41.5 - - + -
184B VAL* 5.6 0.2 - - + -
217B LEU* 4.0 11.7 - - + -
218B PRO 3.1 7.8 + - - +
219B LEU* 3.2 25.7 - - + -
220B ILE* 2.9 25.3 + - - +
248B LEU* 1.3 80.9 - - - +
250B VAL* 1.3 70.4 + - - +
251B ALA* 4.8 0.9 - - + +
268B CYS* 3.9 22.0 - - - -
269B THR 3.3 9.4 - - - +
270B LEU* 3.8 16.2 - - + -
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Residues in contact with VAL 250 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92B LEU* 3.8 22.0 - - + -
93B PHE* 4.2 22.4 - - + -
220B ILE* 3.3 15.9 - - + +
222B ILE* 3.7 24.5 - - + -
238B LEU* 3.9 21.8 - - + -
248B LEU* 5.0 7.9 - - + -
249B ILE* 1.3 83.9 - - - +
251B ALA* 1.3 64.7 + - - +
252B SER* 4.4 0.8 + - - +
267B ALA 3.4 1.4 - - - +
268B CYS* 3.4 4.9 - - - -
269B THR* 2.8 40.1 + - + +
271B VAL* 5.5 0.4 - - + -
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Residues in contact with ALA 251 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113B GLY* 4.1 3.5 - - - +
116B ALA* 3.9 16.2 - - + +
117B LEU* 3.6 39.7 - - + +
219B LEU* 4.4 5.2 - - + +
220B ILE 2.8 11.2 + - - +
221B ASP* 3.5 6.1 - - - +
222B ILE 2.9 25.8 + - - +
249B ILE* 4.2 2.6 - - + -
250B VAL* 1.3 71.5 - - - +
252B SER* 1.3 61.0 + - - +
267B ALA 3.4 4.9 - - - -
268B CYS* 5.4 0.4 - - - -
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Residues in contact with SER 252 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84B PHE* 6.0 0.2 - - - -
88B THR* 3.4 23.9 - - - +
92B LEU* 4.2 15.9 - - - +
113B GLY* 3.3 9.5 - - - -
222B ILE* 3.3 21.1 - - - -
250B VAL* 3.9 3.7 + - - +
251B ALA* 1.3 74.8 - - - +
253B SER* 1.3 60.9 + - - +
254B CYS* 6.5 0.4 - - - -
266B GLY* 3.1 4.1 - - - -
267B ALA* 2.9 38.0 + - - +
269B THR* 5.2 0.3 + - - -
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Residues in contact with SER 253 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113B GLY* 4.0 0.9 - - - -
222B ILE 3.1 10.2 + - - +
223B ALA* 3.8 31.6 - - - +
252B SER* 1.3 77.4 - - - +
254B CYS* 1.3 63.9 + - - +
255B SER* 3.0 20.7 + - - -
256B LLP 2.4 34.9 + - - -
257B ASN* 3.6 16.5 + - - +
265B VAL 3.8 4.6 + - - -
266B GLY* 4.1 0.4 - - - -
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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