Contacts of the strand formed by residues 325 - 342 (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 VAL 325 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3A SER* 2.9 37.7 - - - +
4A LEU* 4.0 17.7 - - + -
308A GLY* 3.2 3.1 - - - -
309A ALA* 2.8 35.1 + - + +
323A GLU 4.7 1.1 - - - +
324A PRO* 1.3 76.3 - - - +
326A LEU* 1.3 64.4 + - - +
327A LEU* 3.4 0.7 + - - +
372A ALA* 3.2 23.3 - - - +
373A PHE* 3.5 25.4 - - + -
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Residues in contact with LEU 326 (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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3A SER 3.5 19.5 + - - +
4A LEU* 4.5 2.4 + - - +
299A THR* 4.7 4.3 - - + +
306A ASP* 3.6 25.6 - - + +
307A LEU 3.5 10.8 - - - +
308A GLY* 4.5 0.7 - - - -
324A PRO 4.1 1.6 + - - -
325A VAL* 1.3 74.5 - - - +
327A LEU* 1.3 58.9 + - - +
328A ALA* 3.4 26.5 - - - +
329A LYS* 4.0 22.0 - - + +
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Residues in contact with LEU 327 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A SER* 3.0 48.7 - - - +
6A VAL* 5.6 3.3 - - + +
9A LYS* 4.7 5.4 + - - -
296A THR* 3.7 29.8 - - + -
307A LEU* 2.8 27.0 + - + +
308A GLY 4.4 0.7 - - - -
309A ALA* 3.9 26.9 - - + +
325A VAL 3.4 0.2 + - - -
326A LEU* 1.3 74.5 - - - +
328A ALA* 1.3 63.4 + - - +
352A CYS* 4.6 2.9 - - - -
365A LEU* 4.0 25.6 - - + +
367A PHE* 4.1 23.1 - - + -
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Residues in contact with ALA 328 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A LYS* 4.4 10.8 - - - +
306A ASP* 3.2 4.9 - - - -
307A LEU* 3.0 30.1 + - + -
326A LEU* 3.4 6.8 - - - +
327A LEU* 1.3 83.2 - - - +
329A LYS* 1.3 62.3 + - - +
332A CYS* 3.8 13.0 - - - -
354A TYR* 3.3 34.1 - - + +
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Residues in contact with LYS 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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9A LYS* 5.7 0.4 - - - +
306A ASP* 3.4 10.8 - - - +
326A LEU* 4.0 18.6 - - + +
328A ALA* 1.3 78.5 - - - +
330A GLY* 1.3 63.4 + - - +
331A SER 5.0 0.5 - - - +
332A CYS* 4.6 2.1 - - - -
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Residues in contact with GLY 330 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305A ALA* 3.2 7.1 - - - -
306A ASP* 2.8 37.1 + - - -
329A LYS* 1.3 76.7 - - - +
331A SER* 1.3 65.9 + - - -
332A CYS* 3.3 3.1 + - - -
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Residues in contact with SER 331 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304A ARG 3.7 10.6 + - - -
305A ALA* 4.4 1.8 - - - +
329A LYS 5.0 0.7 - - - +
330A GLY* 1.3 68.8 - - - -
332A CYS* 1.3 68.2 + - - +
356A ALA* 3.4 3.3 - - - +
357A ASN* 3.2 23.2 + - - -
358A ASP* 2.8 36.5 + - - -
359A TYR* 4.7 1.2 + - - -
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Residues in contact with CYS 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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298A PRO* 3.5 6.3 - - + +
304A ARG* 3.0 30.9 + - - +
305A ALA 4.7 0.7 - - - -
306A ASP 4.5 1.8 - - - +
307A LEU* 3.7 43.5 - - + +
328A ALA* 3.8 14.6 - - - -
329A LYS 4.6 1.6 - - - -
330A GLY 3.3 14.0 + - - +
331A SER* 1.3 84.3 + - - +
333A ALA* 1.3 61.4 + - - +
354A TYR* 3.9 19.3 - - + -
355A GLU 3.2 11.2 - - - +
356A ALA* 4.9 0.4 - - - -
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Residues in contact with ALA 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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272A CYS* 3.7 21.5 - - - -
273A GLN 4.1 1.6 - - - +
298A PRO* 3.9 12.0 - - - +
304A ARG* 4.3 2.7 - - + -
307A LEU* 4.3 8.5 - - - +
332A CYS* 1.3 76.2 - - - +
334A TYR* 1.3 75.6 + - + +
335A SER* 3.7 0.7 + - - -
354A TYR* 5.3 0.2 - - - -
355A GLU* 3.0 29.8 + - + +
359A TYR* 3.5 28.3 - - + +
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Residues in contact with TYR 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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21A ARG* 3.3 22.4 + - - -
22A ILE* 3.8 28.0 - - + +
23A PRO* 3.9 10.5 - - + +
161A PRO* 4.0 14.6 - - + -
218A GLU* 2.5 39.2 + - - -
237A ARG* 3.0 10.3 + - - -
272A CYS* 4.0 6.3 - - - -
273A GLN* 3.2 39.5 - - + +
304A ARG* 4.0 17.0 + - - -
333A ALA* 1.3 82.7 - - + +
335A SER* 1.3 59.1 + - - +
354A TYR* 3.1 2.6 - - - +
355A GLU* 2.8 44.3 + - + +
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Residues in contact with SER 335 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A PRO* 4.2 4.8 - - - +
273A GLN* 2.9 30.8 + - - -
274A GLY* 4.4 1.0 - - - -
275A SER* 3.5 6.4 + - - -
296A THR* 2.8 40.1 + - - -
297A HIS* 4.7 0.5 - - - -
307A LEU* 4.3 10.1 - - - +
333A ALA 3.7 0.9 + - - -
334A TYR* 1.3 76.5 - - - +
336A ASP* 1.3 63.0 + - - +
352A CYS* 4.3 5.4 - - - -
353A LEU 3.0 12.6 - - - -
354A TYR* 3.7 11.7 - - - -
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Residues in contact with ASP 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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23A PRO 3.9 14.8 - - - +
24A ALA* 4.2 0.9 - - - -
25A LEU* 2.7 38.0 + - + +
162A GLY* 3.3 8.3 - - - -
163A HIS* 2.7 48.6 + - - -
220A GLN* 2.9 11.5 + - - -
275A SER* 3.3 2.6 + - - -
335A SER* 1.3 76.5 - - - +
337A LEU* 1.3 64.5 + - - +
351A GLY 3.9 0.2 - - - +
352A CYS* 3.3 5.5 - - - -
353A LEU* 2.8 32.4 + - + +
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Residues in contact with LEU 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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163A HIS* 3.3 12.6 - - - -
275A SER* 2.9 24.2 + - - +
277A ILE* 3.5 16.8 - - + +
294A LEU* 3.6 49.4 - - + +
296A THR* 3.5 43.7 - - + +
336A ASP* 1.3 74.2 + - - +
338A GLN* 1.3 79.2 + - - +
350A PHE* 5.2 1.3 - - + -
351A GLY 3.4 6.5 - - - +
352A CYS* 3.7 22.4 - - + -
367A PHE* 4.8 4.7 - - + -
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Residues in contact with GLN 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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25A LEU* 3.1 45.5 - - + +
26A LEU* 3.5 13.1 - - - +
27A TYR* 2.9 38.1 + - + +
34A LEU* 4.6 3.1 - - + -
163A HIS* 3.3 22.2 + - - +
277A ILE* 4.0 8.3 - - - +
337A LEU* 1.3 89.7 - - - +
339A SER* 1.3 67.3 + - - +
340A MET* 3.9 0.6 - - + +
350A PHE* 3.5 3.3 - - - +
351A GLY 2.9 31.5 + - - +
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Residues in contact with SER 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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27A TYR* 3.4 22.5 - - - +
277A ILE* 3.8 15.1 - - - +
278A SER 4.7 5.2 + - - -
279A PHE* 4.6 13.0 - - - -
280A PRO* 6.0 1.2 - - - +
338A GLN* 1.3 75.4 + - - +
340A MET* 1.3 58.4 + - - +
341A GLY 3.7 5.2 + - - -
348A PRO* 6.4 0.4 - - - -
349A LEU 3.6 8.5 - - - -
350A PHE* 4.0 11.4 - - - -
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Residues in contact with MET 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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27A TYR* 3.5 44.7 + - + -
34A LEU* 3.5 35.7 - - + -
59A TYR* 4.6 11.3 - - + -
66A VAL* 4.0 7.4 - - + -
338A GLN 3.9 8.5 - - - +
339A SER* 1.3 76.7 - - - +
341A GLY* 1.3 63.5 + - - +
342A THR 3.9 1.2 + - - +
349A LEU* 2.8 32.6 + - + +
350A PHE 3.8 4.3 - - - -
351A GLY* 3.6 27.6 - - - +
366A MET* 3.7 28.0 - - - +
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Residues in contact with GLY 341 (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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27A TYR* 4.3 5.3 - - - -
339A SER* 3.7 5.9 + - - +
340A MET* 1.3 77.0 - - - +
342A THR* 1.3 60.8 + - - -
348A PRO* 3.7 5.2 - - - +
349A LEU 2.9 23.0 + - - +
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Residues in contact with THR 342 (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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59A TYR* 4.9 6.2 + - - -
340A MET 3.9 1.1 + - - +
341A GLY* 1.3 73.5 - - - -
343A GLY* 1.3 75.6 + - - +
346A GLY* 3.5 28.9 - - - +
347A SER 3.9 3.8 - - - +
348A PRO* 4.6 1.9 - - - +
349A LEU* 3.9 8.3 - - - +
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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