Contacts of the strand formed by residues 348 - 356 (chain A) in PDB entry 2F24
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 PRO 348 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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279A PHE* 4.2 23.3 - - + -
280A PRO* 4.7 6.7 - - + +
282A PRO* 5.0 7.0 - - + -
341A GLY 3.7 8.1 - - - +
342A THR* 4.6 1.6 - - + +
346A GLY 4.7 0.9 - - - +
347A SER* 1.3 87.3 - - - +
349A LEU* 1.3 59.5 + - - +
350A PHE* 3.7 26.8 - - + -
368A THR* 3.1 5.9 - - - -
369A LEU* 3.0 31.7 + - + -
377A TYR* 3.7 11.2 - - - +
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Residues in contact with LEU 349 (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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7A LEU* 3.5 31.9 - - + -
59A TYR* 4.0 33.2 - - + +
339A SER* 3.6 1.4 - - - -
340A MET* 2.8 51.3 + - + +
341A GLY 2.9 17.0 + - - +
342A THR 3.9 7.0 - - - +
343A GLY* 3.6 13.0 - - - +
347A SER 3.4 0.6 + - - -
348A PRO* 1.3 73.7 - - - +
350A PHE* 1.3 71.4 + - - +
366A MET* 3.7 21.8 - - + -
367A PHE 3.8 6.1 - - - +
368A THR* 3.9 7.0 - - + +
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Residues in contact with PHE 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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277A ILE* 3.8 18.6 - - + -
279A PHE* 3.8 41.1 - + + -
294A LEU* 3.6 28.5 - - + -
337A LEU* 5.2 1.3 - - + -
338A GLN 3.5 2.5 - - - +
339A SER* 4.0 7.6 - - - -
340A MET* 3.8 5.4 - - - +
348A PRO* 3.7 33.2 - - + -
349A LEU* 1.3 81.2 - - - +
351A GLY* 1.3 63.0 + - - +
365A LEU 3.8 0.2 - - - +
366A MET* 3.2 8.7 - - - +
367A PHE* 2.8 65.3 + + + +
369A LEU* 3.9 24.5 - - + -
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Residues in contact with GLY 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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25A LEU* 3.4 11.2 - - - +
337A LEU* 3.4 6.4 - - - +
338A GLN 2.9 33.7 + - - +
340A MET* 3.6 17.7 - - - -
350A PHE* 1.3 75.8 - - - +
352A CYS* 1.3 60.2 + - - +
364A PHE* 3.8 9.2 - - - -
365A LEU 3.4 5.4 - - - -
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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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25A LEU* 3.9 1.2 - - - +
296A THR* 4.1 19.5 - - - -
307A LEU* 4.2 19.1 - - - -
327A LEU* 4.6 3.1 - - - -
335A SER* 4.3 2.5 - - - -
336A ASP 3.3 7.6 - - - -
337A LEU* 3.7 22.2 - - + -
351A GLY* 1.3 74.6 - - - +
353A LEU* 1.3 68.9 + - - +
354A TYR* 4.4 4.1 - - - -
363A VAL 3.5 1.6 - - - +
364A PHE* 3.3 8.1 - - - -
365A LEU* 2.8 46.6 + - + +
367A PHE* 4.3 12.6 - - + -
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Residues in contact with LEU 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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12A VAL* 3.7 29.4 - - + -
13A PHE* 5.0 0.9 - - + -
23A PRO* 3.7 19.8 - - + +
24A ALA 3.5 27.6 - - - +
25A LEU* 4.3 11.8 - - + +
36A ALA* 3.7 22.2 - - + -
37A PHE 4.0 5.4 - - - +
68A TRP* 5.3 0.2 - - + -
335A SER* 3.0 3.5 - - - -
336A ASP* 2.8 36.1 + - + +
352A CYS* 1.3 73.3 - - - +
354A TYR* 1.3 61.0 + - - +
362A ILE* 3.7 14.1 - - + -
363A VAL 3.3 8.3 - - - +
364A PHE* 4.0 17.5 - - + -
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Residues in contact with TYR 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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9A LYS* 3.7 21.0 + - - -
23A PRO* 4.3 1.8 - - - -
307A LEU* 3.5 22.2 - - + -
328A ALA* 3.3 22.3 - - + +
332A CYS* 3.9 19.1 - - + -
333A ALA 5.2 0.4 - - - +
334A TYR 3.1 11.4 - - - +
335A SER* 3.7 12.1 - - - -
352A CYS* 4.4 6.1 - - - -
353A LEU* 1.3 78.0 - - - +
355A GLU* 1.3 73.5 + - - +
356A ALA* 3.6 20.8 + - + +
362A ILE* 3.3 5.9 - - - +
363A VAL* 2.8 60.8 + - + +
365A LEU* 3.3 32.7 - - + +
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Residues in contact with GLU 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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20A TYR 5.5 0.2 - - - +
21A ARG* 2.7 49.5 + - + +
22A ILE* 2.7 22.0 + - - +
23A PRO* 3.6 16.6 - - + -
332A CYS* 3.2 5.0 - - - -
333A ALA* 3.0 34.3 + - + +
334A TYR* 2.8 36.3 + - - +
354A TYR* 1.3 79.0 - - - +
356A ALA* 1.3 57.9 + - - +
359A TYR* 3.6 11.7 - - + -
361A GLU 3.5 8.3 - - - +
362A ILE* 4.4 7.4 - - + +
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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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331A SER* 3.4 11.2 - - - +
332A CYS* 4.4 0.9 - - - +
354A TYR* 3.6 22.9 - - + +
355A GLU* 1.3 76.5 - - - +
357A ASN* 1.3 77.4 + - + +
358A ASP 3.5 1.8 - - - -
359A TYR 3.3 3.0 + - - +
360A GLU 3.2 14.0 + - - -
361A GLU* 2.9 16.7 + - + +
363A VAL* 4.0 18.2 - - + -
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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