Contacts of the strand formed by residues 344 - 356 (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 TYR 344 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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191A LYS* 4.0 33.5 + - - -
192A ALA 3.0 23.6 - - - +
193A LYS* 3.7 9.0 - - + -
194A TRP* 3.9 9.0 - - - -
339A ASP* 3.8 11.8 + - - -
341A ASN* 2.7 61.0 + - - +
343A GLU* 1.3 92.4 - - + +
345A THR* 1.3 75.4 + - - +
346A GLU* 3.7 27.8 + - + -
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Residues in contact with THR 345 (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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190A PHE* 3.8 6.7 - - + -
191A LYS* 3.4 2.6 - - - -
192A ALA 3.0 27.7 + - - -
194A TRP* 3.3 16.1 - - - -
244A TYR* 2.7 39.3 + - - +
338A ILE* 4.1 14.6 - - + -
339A ASP 3.0 10.3 - - - +
340A VAL* 3.9 8.8 - - + +
344A TYR* 1.3 77.5 + - - +
346A GLU* 1.3 67.0 + - - +
374B ILE* 3.8 21.5 - - + -
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Residues in contact with GLU 346 (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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166A GLU* 4.3 2.6 - - - +
168A LYS* 3.5 34.3 + - + -
189A TYR* 2.4 40.0 + - + +
190A PHE 3.4 6.5 - - - +
191A LYS* 4.2 12.6 + - + +
337A TYR* 3.7 10.3 + - + -
338A ILE* 3.1 2.9 - - - +
339A ASP* 2.7 46.6 + - + +
344A TYR* 3.7 25.6 + - + -
345A THR* 1.3 76.3 - - - +
347A ALA* 1.3 64.5 + - - +
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Residues in contact with ALA 347 (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* 3.8 22.2 - - + -
189A TYR* 3.4 3.1 - - - -
190A PHE* 2.7 46.7 + - + +
337A TYR* 3.2 13.7 - - - +
338A ILE* 4.1 6.1 - - + -
346A GLU* 1.3 76.5 - - - +
348A ALA* 1.3 64.8 + - - +
374B ILE* 4.5 6.7 - - + -
384B PHE* 4.0 19.3 - - + -
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Residues in contact with ALA 348 (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* 4.5 1.2 - - - -
165A THR* 4.0 9.6 - - - -
168A LYS* 3.9 27.1 - - + -
169A ILE* 3.9 11.2 - - + -
188A VAL 3.3 14.4 - - - +
189A TYR* 4.1 6.3 - - + -
336A THR* 3.2 2.8 - - - -
337A TYR* 2.7 34.0 + - + +
347A ALA* 1.3 78.6 - - - +
349A ALA* 1.3 61.8 + - - +
384B PHE* 4.2 4.7 - - - -
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Residues in contact with ALA 349 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A SER* 3.5 31.2 - - - -
56A SER* 4.2 1.3 + - - +
165A THR* 4.6 0.3 - - - +
169A ILE* 4.0 6.0 - - - +
187A ALA* 3.3 2.3 - - - +
188A VAL* 2.8 37.8 + - + +
334A HIS* 3.9 5.8 - - + -
335A LYS 3.1 13.7 - - - +
336A THR* 3.7 11.2 - - + -
348A ALA* 1.3 78.4 - - - +
350A ALA* 1.3 60.9 + - - +
384B PHE* 4.3 1.6 - - + -
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Residues in contact with ALA 350 (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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56A SER* 4.1 0.7 - - - -
161A VAL* 3.8 18.6 - - + -
169A ILE* 3.7 24.9 - - + +
172A LEU* 4.0 15.9 - - + +
186A SER 2.9 14.6 - - - +
187A ALA* 4.3 1.8 - - + -
333A ILE 4.1 0.2 - - - +
334A HIS* 3.4 3.6 + - - -
335A LYS 2.9 30.5 + - - +
349A ALA* 1.3 75.8 - - - +
351A THR* 1.3 62.8 + - - +
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Residues in contact with THR 351 (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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56A SER* 2.8 30.1 + - - -
57A ILE* 4.2 7.6 - - + -
60A VAL* 3.4 12.1 - - + +
172A LEU* 4.8 0.9 - - - -
185A ILE* 3.2 6.6 - - - +
186A SER 2.8 33.0 + - - +
299A LEU* 4.5 1.6 - - + -
332A MET* 3.7 30.3 - - + -
333A ILE 3.3 13.2 - - - +
334A HIS* 2.7 27.0 + - - +
350A ALA* 1.3 72.3 - - - +
352A CYS* 1.3 65.5 + - - +
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Residues in contact with CYS 352 (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* 4.0 15.7 - - + -
173A LEU* 3.9 19.3 - - - -
183A LEU* 3.8 27.8 - - - -
184A ALA 3.4 3.8 - - - -
185A ILE* 4.0 12.3 - - + -
331A ALA 3.8 0.5 - - - +
332A MET* 3.1 7.1 - - - -
333A ILE* 2.9 48.5 + - + +
351A THR* 1.3 78.0 - - - +
353A ALA* 1.3 64.9 + - - +
354A LEU* 4.2 3.3 + - - -
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Residues in contact with ALA 353 (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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60A VAL* 3.6 24.0 - - + +
64A LEU* 4.1 24.5 - - + -
182A LEU 3.8 1.0 - - - +
183A LEU* 3.6 4.9 - - - +
184A ALA* 3.1 30.3 + - + +
329A VAL* 4.3 7.0 - - + -
331A ALA 3.3 9.6 - - - +
332A MET* 4.2 8.7 - - - -
352A CYS* 1.3 75.7 - - - +
354A LEU* 1.3 58.8 + - - +
355A VAL* 3.9 2.8 + - - +
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Residues in contact with LEU 354 (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* 5.4 6.3 - - - +
178A LEU* 3.4 34.5 - - + -
179A SER* 5.1 3.1 - - - +
180A THR* 3.7 26.9 - - + +
183A LEU* 3.6 18.2 - - + -
329A VAL* 3.6 2.6 - - - -
330A ASP* 3.0 31.3 + - + -
331A ALA* 3.1 21.4 + - + +
352A CYS* 4.1 4.0 - - - -
353A ALA* 1.3 71.3 - - - +
355A VAL* 1.3 60.9 + - - +
356A ALA* 4.1 17.9 - - + -
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Residues in contact with VAL 355 (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* 4.2 15.0 - - + -
180A THR* 3.6 2.6 - - - +
181A CYS* 2.6 32.7 + - + -
182A LEU* 2.8 40.0 + - + +
184A ALA* 6.0 1.3 - - + +
321A MET* 4.3 14.1 - - + -
327A VAL* 3.4 38.1 - - + -
328A SER 3.1 13.2 - - - +
329A VAL* 3.3 24.0 - - + +
353A ALA 4.8 3.1 - - - +
354A LEU* 1.3 72.1 - - - +
356A ALA* 1.3 53.3 + - - +
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Residues in contact with ALA 356 (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* 3.0 32.5 - - + +
180A THR* 4.0 2.9 - - - +
181A CYS* 3.8 3.4 - - - +
327A VAL* 3.1 5.0 - - - +
328A SER 2.4 48.1 + - - -
330A ASP* 3.5 19.3 - - - +
354A LEU* 3.9 11.6 + - + -
355A VAL* 1.3 70.7 - - - +
357A ASP* 1.3 69.6 + - - +
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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