Contacts of the strand formed by residues 248 - 255 (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 THR 248 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103A ASP* 3.6 7.8 + - - +
111A SER* 4.4 6.7 + - - -
190A PHE* 3.4 26.3 - - + -
243A PRO* 3.9 1.4 - - - +
244A TYR* 2.8 39.0 + - - +
245A VAL 4.8 0.7 + - - -
246A GLY 3.6 1.4 - - - +
247A ASP* 1.3 85.6 + - - +
249A SER* 1.3 64.2 + - - +
374B ILE* 5.2 0.9 - - - -
375B ARG 3.3 13.9 - - - +
376B HIS* 3.5 32.5 - - + +
377B VAL* 4.2 3.2 - - - +
383B LEU* 4.1 10.1 - - + -
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Residues in contact with SER 249 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241A GLU* 2.7 37.7 + - - +
242A LEU 3.3 13.9 - - - -
243A PRO* 3.7 7.0 - - - -
244A TYR* 3.5 10.0 - - - -
248A THR* 1.3 78.1 - - - +
250A MET* 1.3 60.3 + - - +
251A VAL* 4.0 3.2 + - - +
373B VAL 3.6 0.5 - - - +
374B ILE* 3.5 3.5 - - - +
375B ARG* 3.0 42.9 + - - +
377B VAL* 5.0 5.7 - - - +
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Residues in contact with MET 250 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194A TRP* 3.6 30.5 - - + -
240A ILE 3.8 1.0 - - - +
241A GLU* 3.6 0.2 - - - -
242A LEU* 2.7 50.8 + - + +
244A TYR* 3.5 21.4 - - + +
249A SER* 1.3 73.8 - - - +
251A VAL* 1.3 63.2 + - - +
252A VAL* 3.6 25.6 + - + -
288A ILE* 5.1 10.3 - - + -
291A PHE* 5.5 4.0 - - + -
340A VAL* 4.8 17.3 - - + -
370B PHE* 5.9 1.1 - - + -
372B TYR* 3.9 26.2 - - + -
373B VAL 3.3 11.0 - - - +
374B ILE* 4.5 6.5 - - + +
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Residues in contact with VAL 251 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239A ILE* 3.6 34.1 - - + -
240A ILE 3.1 9.2 - - - +
241A GLU* 4.4 12.1 - - + +
249A SER* 4.3 9.0 - - - +
250A MET* 1.3 73.5 - - - +
252A VAL* 1.3 63.7 + - - +
253A ILE* 4.8 1.8 - - + +
272A PHE* 3.7 23.3 - - + -
276A CYS* 4.3 11.0 - - - -
279A MET* 5.1 1.3 - - - -
371B ILE 3.9 0.5 - - - +
372B TYR* 3.3 1.7 - - - -
373B VAL* 2.7 41.9 + - - +
375B ARG* 3.8 28.5 - - - +
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Residues in contact with VAL 252 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238A SER 3.6 1.0 - - - +
239A ILE* 3.3 5.2 - - - +
240A ILE* 2.8 42.7 + - + -
242A LEU* 4.4 7.2 - - + -
250A MET* 3.6 36.6 - - + +
251A VAL* 1.3 75.2 - - - +
253A ILE* 1.3 63.4 + - - +
254A LEU 4.0 0.2 - - - -
288A ILE* 4.5 6.7 - - + -
364B PHE* 3.5 30.0 - - + -
370B PHE* 3.7 29.2 - - + -
371B ILE 3.3 10.5 - - - +
372B TYR* 4.4 3.1 - - + -
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Residues in contact with ILE 253 (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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237A PHE* 3.6 26.5 - - + -
238A SER 3.5 3.6 - - - -
239A ILE* 3.7 23.1 - - + -
251A VAL* 4.8 2.9 - - + +
252A VAL* 1.3 72.4 - - - +
254A LEU* 1.3 59.8 + - - +
255A PRO* 3.6 4.3 - - + +
260A LEU* 4.5 1.1 - - + +
263A ILE* 4.0 21.8 - - + -
267A LEU* 4.2 6.7 - - + -
272A PHE* 4.1 29.8 - - + -
275A TRP* 4.2 13.7 - - + -
370B PHE* 3.4 6.7 - - - +
371B ILE* 2.9 58.1 + - + +
373B VAL* 5.1 1.1 - - + -
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Residues in contact with LEU 254 (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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237A PHE* 3.7 2.5 - - - -
238A SER* 2.8 35.3 + - - +
252A VAL 3.9 0.6 + - - -
253A ILE* 1.3 74.4 - - - +
255A PRO* 1.3 74.5 - - - +
256A ASP* 4.2 1.0 - - - +
360B VAL* 5.1 9.6 - - + -
364B PHE* 3.6 28.7 - - + -
365B CYS 3.2 35.4 - - - +
366B ALA* 3.7 16.4 - - + -
368B HIS* 3.6 43.3 - - + +
369B PRO 4.0 1.1 - - - +
370B PHE* 3.9 11.4 - - + -
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Residues in contact with PRO 255 (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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236A ASN 3.6 8.3 - - - +
237A PHE* 3.7 5.3 - - + -
253A ILE* 3.6 8.5 - - + +
254A LEU* 1.3 89.2 - - + +
256A ASP* 1.3 56.5 + - - +
257A ASN* 3.5 19.1 - - + +
259A GLY* 3.8 13.7 - - - +
260A LEU* 3.6 35.9 - - + +
263A ILE* 4.1 9.2 - - + -
368B HIS* 2.7 28.4 + - + +
369B PRO 3.3 21.8 - - - +
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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
------------------------------------------------------------
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