Contacts of the strand formed by residues 328 - 340 (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 SER 328 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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313A GLY 3.8 13.3 + - - -
314A SER* 3.5 24.5 + - - -
316A GLY 4.6 0.4 + - - -
318A TYR* 5.0 3.1 - - - -
326A ASP* 4.0 1.4 + - - -
327A VAL* 1.3 77.4 + - - +
329A VAL* 1.3 62.8 + - - +
330A ASP* 3.6 18.8 + - - +
355A VAL* 3.1 2.2 - - - -
356A ALA* 2.4 44.0 + - - -
357A ASP* 3.5 20.5 + - - +
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Residues in contact with VAL 329 (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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64A LEU* 4.0 11.4 - - + -
311A VAL 4.0 10.5 + - - +
312A PHE* 3.4 32.2 - - + +
313A GLY 2.9 25.3 + - - +
318A TYR* 3.9 28.6 - - + +
328A SER* 1.3 71.9 - - - +
330A ASP* 1.3 61.3 + - - +
331A ALA 4.1 14.4 - - - +
353A ALA* 4.3 13.2 - - + -
354A LEU 3.6 7.2 - - - +
355A VAL* 3.3 28.5 - - + -
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Residues in contact with ASP 330 (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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179A ASP* 4.7 3.6 - - - -
300A VAL* 5.4 2.8 - - - +
312A PHE* 5.7 1.1 - - - -
313A GLY* 3.6 12.5 - - - +
314A SER 4.7 0.3 + - - -
328A SER* 3.6 21.8 - - - +
329A VAL* 1.3 79.0 - - - +
331A ALA* 1.3 64.9 + - - +
354A LEU* 3.0 15.7 + - + +
356A ALA* 3.5 23.4 - - - +
357A ASP* 4.8 1.6 + - - +
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Residues in contact with ALA 331 (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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175A GLU* 5.7 5.4 - - - +
298A ASN* 6.0 2.9 - - - +
300A VAL* 4.3 11.5 - - - +
329A VAL* 3.6 7.4 + - - +
330A ASP* 1.3 80.8 - - - +
332A MET* 1.3 63.7 + - - +
333A ILE* 4.3 0.9 - - + +
352A CYS 4.3 0.7 - - - -
353A ALA* 3.3 3.1 - - - +
354A LEU* 3.1 40.5 + - + -
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Residues in contact with MET 332 (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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57A ILE* 4.0 7.6 - - + +
60A VAL* 4.0 11.4 - - + -
61A LEU* 3.5 39.0 - - + -
64A LEU* 4.8 0.9 - - - -
298A ASN* 3.7 4.9 + - - -
299A LEU* 2.9 50.0 + - + +
300A VAL* 3.9 10.6 - - + +
303A LEU* 4.0 3.4 - - + -
312A PHE* 4.0 27.6 - - + -
331A ALA* 1.3 78.1 - - - +
333A ILE* 1.3 60.0 + - - +
351A THR* 3.7 24.7 - - + -
352A CYS 3.1 11.0 - - - +
353A ALA* 4.2 11.7 - - - -
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Residues in contact with ILE 333 (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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172A LEU* 4.1 18.4 - - + +
173A LEU* 5.6 2.9 - - + -
296A SER* 3.8 17.5 - - - +
297A TYR 2.9 31.4 - - - +
298A ASN* 4.1 5.4 - - + +
299A LEU* 4.9 0.7 - - - -
331A ALA* 5.5 0.2 - - - +
332A MET* 1.3 74.6 - - - +
334A HIS* 1.3 59.8 + - - +
335A LYS* 4.1 21.1 - - + -
351A THR* 3.3 8.2 - - - +
352A CYS* 2.9 53.2 + - + +
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Residues in contact with HIS 334 (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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52A ILE* 3.7 20.1 - - + +
53A SER 3.0 42.4 + - - -
56A SER* 3.8 8.1 - - - -
57A ILE* 3.6 14.9 - - + +
296A SER* 3.5 1.0 - - - -
297A TYR* 2.8 41.8 + + + +
299A LEU* 4.1 21.8 - - + -
333A ILE* 1.3 75.7 - - - +
335A LYS* 1.3 60.5 + - - +
336A THR* 3.5 21.5 - - + +
349A ALA* 3.9 11.2 - - + -
350A ALA 3.4 4.8 + - - -
351A THR* 2.7 27.9 + - - -
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Residues in contact with LYS 335 (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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169A ILE* 3.7 21.0 - - + +
171A PRO* 3.0 24.8 + - - +
172A LEU* 3.3 26.9 + - + +
174A ASP* 2.6 31.7 + - - -
295A GLY 3.2 7.0 - - - +
296A SER* 3.4 28.7 - - - +
333A ILE* 4.1 16.2 - - + -
334A HIS* 1.3 73.4 - - - +
336A THR* 1.3 65.6 + - - +
349A ALA* 3.1 3.6 - - - +
350A ALA 2.9 32.9 + - - +
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Residues in contact with THR 336 (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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51A PHE* 2.8 45.2 + - + +
52A ILE* 3.9 4.7 - - - -
53A SER 4.4 0.2 - - - +
169A ILE* 3.7 5.4 - - - +
294A THR* 3.1 7.7 - - - -
295A GLY* 2.9 41.8 + - - +
297A TYR* 3.9 1.7 - - + -
334A HIS* 3.5 28.0 - - + +
335A LYS* 1.3 81.4 - - - +
337A TYR* 1.3 64.7 + - - +
348A ALA 3.2 7.4 - - - -
349A ALA* 3.7 8.5 - - + -
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Residues in contact with TYR 337 (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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51A PHE* 3.4 7.4 - - - -
168A LYS* 3.5 71.9 + - + +
169A ILE* 4.1 0.7 - - + -
292A LYS* 3.2 36.4 - - + -
293A VAL 3.3 7.6 - - - -
294A THR* 3.6 22.7 - - + -
336A THR* 1.3 78.0 - - - +
338A ILE* 1.3 65.7 + - - +
339A ASP* 3.5 18.7 + - + +
346A GLU* 3.7 20.4 + - - -
347A ALA* 3.2 5.3 - - - -
348A ALA 2.7 36.2 + - - +
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Residues in contact with ILE 338 (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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51A PHE* 3.5 26.7 - - + -
250A MET* 5.7 0.4 - - - -
291A PHE* 4.0 7.0 - - + -
292A LYS* 3.3 5.7 - - - +
293A VAL* 2.9 51.2 + - + +
337A TYR* 1.3 81.0 - - - +
339A ASP* 1.3 63.8 + - - +
340A VAL* 3.8 23.6 - - + -
345A THR* 4.1 3.1 - - + -
346A GLU 3.1 10.3 - - - +
347A ALA* 4.1 3.4 - - + -
372B TYR* 3.6 42.4 - - + +
374B ILE* 4.1 15.7 - - + -
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Residues in contact with ASP 339 (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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290A LYS* 5.9 0.3 - - - +
291A PHE 3.4 3.4 - - - -
292A LYS* 3.8 29.4 + - + +
337A TYR* 3.5 23.2 + - + +
338A ILE* 1.3 75.9 - - - +
340A VAL* 1.3 69.0 + - - +
341A ASN* 3.1 28.3 + - - +
344A TYR* 3.8 14.7 + - - +
345A THR* 3.0 6.6 - - - +
346A GLU* 2.7 43.5 + - + +
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Residues in contact with VAL 340 (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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194A TRP* 4.0 22.9 - - + -
221A MET* 4.1 15.5 - - + -
250A MET* 4.8 12.1 - - + -
288A ILE* 5.6 1.6 - - + -
289A PRO 4.1 8.7 - - - +
290A LYS* 3.6 5.0 - - - +
291A PHE* 2.8 55.4 + - + +
338A ILE* 3.8 25.4 - - + -
339A ASP* 1.3 78.8 + - - +
341A ASN* 1.3 64.3 + - - +
344A TYR 3.9 2.7 - - - -
345A THR* 3.9 10.5 - - + +
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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