Contacts of the strand formed by residues 320 - 333 (chain A) in PDB entry 1AF6
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 MET 320 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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316A TRP* 3.2 38.2 + - + +
317A THR* 3.1 30.7 + - + +
319A ILE* 1.3 80.3 - - + +
321A SER* 1.3 66.2 + - - +
349A GLN* 3.8 21.1 - - - +
350A GLN 3.3 8.7 - - - +
351A TRP* 3.7 35.0 - - + +
94C TRP* 6.0 7.6 - - + -
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Residues in contact with SER 321 (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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313A MET* 3.1 32.6 - - - +
314A TYR 3.2 16.2 - - - -
315A LYS* 4.1 2.5 - - - -
316A TRP* 4.0 4.7 - - - -
320A MET* 1.3 77.5 - - - +
322A THR* 1.3 62.1 + - - +
323A VAL* 3.8 3.0 - - - +
349A GLN* 3.3 9.2 - - - -
350A GLN* 2.8 40.7 + - - +
352A GLN* 2.9 20.4 + - - -
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Residues in contact with THR 322 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312A PRO 4.2 0.5 - - - +
313A MET* 3.5 1.9 - - - -
314A TYR* 2.8 39.8 + - + +
316A TRP* 2.8 28.0 + - + -
321A SER* 1.3 71.7 - - - +
323A VAL* 1.3 64.5 + - - +
324A MET* 5.8 0.7 - - + -
347A LEU* 4.0 22.7 - - + -
348A ALA 3.4 10.5 - - - +
349A GLN* 2.6 22.8 + - - +
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Residues in contact with VAL 323 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A LEU* 4.0 18.1 - - + +
311A ARG* 3.8 25.4 - - + +
312A PRO 3.7 11.7 - - - +
313A MET* 3.9 14.4 - - + -
321A SER* 3.8 17.3 - - - +
322A THR* 1.3 80.5 - - - +
324A MET* 1.3 63.8 + - - +
346A THR 4.0 0.2 - - - +
347A LEU* 3.6 2.9 - - - +
348A ALA* 2.7 47.1 + - + +
350A GLN* 4.0 28.0 - - + +
357A ILE* 5.3 2.9 - - + -
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Residues in contact with MET 324 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A LEU* 4.6 0.4 - - - -
311A ARG* 3.2 10.7 - - - +
312A PRO* 3.0 44.4 + - + +
322A THR* 5.8 0.7 - - + -
323A VAL* 1.3 77.8 - - - +
325A GLU* 1.3 64.5 + - - +
326A ILE* 4.0 30.5 - - + -
345A ILE* 5.2 9.2 - - + -
346A THR 3.1 10.8 - - - +
347A LEU* 3.9 27.8 - - + -
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Residues in contact with GLU 325 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A TYR* 3.3 21.5 - - + +
33A ARG 4.3 0.2 - - - -
34A LEU* 3.0 27.5 + - + +
114A MET* 3.6 19.9 - - + +
310A ILE 3.4 10.3 - - - +
311A ARG* 2.9 37.7 + - - -
324A MET* 1.3 76.2 - - - +
326A ILE* 1.3 67.7 + - - +
327A GLY 4.2 0.4 - - - -
344A LYS* 2.6 33.0 + - - +
345A ILE* 3.4 3.8 - - - +
346A THR* 2.8 37.4 + - - +
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Residues in contact with ILE 326 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A TYR* 4.6 0.7 - - - -
308A VAL 4.8 0.2 - - - -
309A GLY* 3.0 4.5 - - - -
310A ILE* 2.9 56.3 + - + +
324A MET* 4.0 28.3 - - + -
325A GLU* 1.3 80.5 - - - +
327A GLY* 1.3 64.3 + - - +
328A TYR* 6.3 0.7 - - + -
343A TYR* 5.8 4.0 - - + -
344A LYS 3.4 8.7 - - - +
345A ILE* 4.4 19.5 - - + -
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Residues in contact with GLY 327 (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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32A TYR* 3.7 32.3 - - - +
308A VAL 3.6 5.8 - - - -
325A GLU 4.2 0.2 - - - -
326A ILE* 1.3 78.2 - - - +
328A TYR* 1.3 61.4 + - - -
329A ASP* 5.2 0.6 - - - +
342A GLN 3.8 0.5 - - - +
343A TYR* 3.2 5.2 - - - +
344A LYS* 2.8 40.3 + - - +
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Residues in contact with TYR 328 (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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32A TYR* 3.8 1.4 - - - -
306A TRP* 5.0 6.5 - - + -
307A THR* 3.3 9.1 - - - +
308A VAL* 2.8 53.9 + - + +
326A ILE* 6.3 0.4 - - + -
327A GLY* 1.3 75.0 - - - +
329A ASP* 1.3 73.0 + - - +
330A ASN* 3.2 38.5 + - + +
341A ASN* 4.0 15.2 - - + +
342A GLN 3.3 16.2 - - - -
343A TYR* 4.2 14.1 - + + -
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Residues in contact with ASP 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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25A THR* 3.2 34.2 + - + +
28A ALA* 4.2 4.5 - - - +
30A SER* 4.6 8.0 + - - +
31A LYS* 5.1 2.3 - - - -
32A TYR* 3.9 16.2 - - - -
305A TRP* 3.2 17.9 + - - +
306A TRP 3.6 3.4 - - - -
307A THR* 2.7 27.6 - - - +
327A GLY 5.2 0.5 - - - +
328A TYR* 1.3 81.4 - - - +
330A ASN* 1.3 62.1 + - - +
340A ASN 4.4 0.4 - - - -
341A ASN* 3.1 7.1 - - - +
342A GLN* 2.9 42.4 + - - +
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Residues in contact with ASN 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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304A LYS 3.8 1.4 - - - +
305A TRP* 3.4 2.5 - - - -
306A TRP* 2.9 53.3 + - + +
328A TYR* 3.2 30.8 + - + +
329A ASP* 1.3 75.5 - - - +
331A VAL* 1.3 66.9 + - - +
332A GLU* 4.5 1.6 + - - +
339A LYS* 3.7 35.7 - - - +
340A ASN 3.3 3.4 + - - -
341A ASN* 3.7 14.6 + - - +
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Residues in contact with VAL 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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25A THR* 3.6 25.8 - - + -
26A THR 3.9 7.4 - - - +
27A GLY* 3.8 18.8 - - - +
28A ALA* 3.6 16.4 - - + +
303A THR* 4.0 13.7 - - - -
304A LYS 3.5 7.9 - - - +
305A TRP* 3.7 20.2 - - + -
330A ASN* 1.3 81.2 + - - +
332A GLU* 1.3 63.1 + - - +
339A LYS* 3.2 1.8 - - - -
340A ASN* 2.7 39.7 + - + +
376A TRP* 3.2 19.1 + - + -
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Residues in contact with GLU 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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303A THR* 3.4 5.0 - - - -
304A LYS* 2.8 65.8 + - + +
330A ASN* 4.2 1.5 + - - +
331A VAL* 1.3 76.0 - - - +
333A SER* 1.3 73.2 + - - +
334A GLN* 5.6 1.4 - - - -
337A GLY* 4.0 11.2 - - - +
338A ASP 3.2 13.9 - - - +
339A LYS* 2.6 40.6 + - + +
376A TRP* 4.2 1.1 - - - -
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Residues in contact with SER 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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301A ASN 5.9 0.2 - - - -
302A GLY 4.1 5.2 + - - -
332A GLU* 1.3 76.1 - - - +
334A GLN* 1.3 62.0 + - - +
335A ARG 3.1 13.9 + - - -
336A THR* 3.3 22.7 + - - -
337A GLY* 2.9 23.4 + - - -
338A ASP 2.9 8.4 + - - -
376A TRP* 3.6 32.3 - - - +
393A ALA* 3.2 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
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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