Contacts of the strand formed by residues 329 - 340 (chain E) in PDB entry 6Q2J
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 PHE 329 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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283E VAL* 4.7 4.5 - - + -
293E VAL* 4.1 18.6 - - + -
318E LEU* 4.0 11.5 - - + +
324E TRP* 5.2 4.9 - + - -
325E ALA 2.7 21.9 + - - +
326E GLN* 4.0 14.2 - - - +
328E THR* 1.3 102.0 - - - +
330E ARG* 1.3 60.9 + - - +
356E LEU* 4.5 22.0 - - + -
357E VAL 3.5 11.0 - - - -
358E LEU* 3.6 24.9 - - + -
359E ASN* 5.0 3.8 + - - -
362E LEU* 5.0 1.3 - - + -
370E MET* 3.8 34.3 - - + -
372E LEU* 4.4 15.3 - - + -
395E VAL* 4.0 23.3 - - + -
397E VAL* 5.0 5.6 - - + -
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Residues in contact with ARG 330 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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289E GLU 4.6 2.6 + - - -
290E ASP* 4.0 12.5 + - - +
318E LEU* 5.0 2.0 - - - -
329E PHE* 1.3 73.5 - - - +
331E VAL* 1.3 66.5 + - - +
332E GLU* 3.6 16.8 + - + +
356E LEU* 3.6 4.4 - - - +
357E VAL* 2.9 64.0 + - + +
358E LEU 3.5 15.4 + - - -
359E ASN* 3.5 29.7 + - - +
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Residues in contact with VAL 331 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316E SER* 4.4 15.8 + - - +
318E LEU* 3.7 42.1 - - + +
330E ARG* 1.3 76.7 - - - +
332E GLU* 1.3 61.4 + - - +
333E HIS 3.8 2.3 + - - -
354E TYR* 4.5 17.5 - - + -
355E ARG 3.4 11.9 - - - +
356E LEU* 3.8 15.7 - - + -
374E VAL* 3.8 30.7 - - + -
393E PHE* 5.6 1.3 - - + -
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Residues in contact with GLU 332 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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330E ARG* 3.6 18.9 + - + +
331E VAL* 1.3 72.0 - - - +
333E HIS* 1.3 62.0 + - - +
334E TRP* 3.2 34.7 + - + -
353E ASP 4.1 0.5 - - - +
354E TYR* 3.7 1.3 - - - -
355E ARG* 2.9 48.2 + - + +
357E VAL* 3.4 26.2 - - + +
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Residues in contact with HIS 333 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310E LEU* 4.4 8.1 - - + +
314E TYR* 4.2 27.9 - - + +
316E SER* 4.1 13.7 - - - +
331E VAL 3.8 1.2 + - - +
332E GLU* 1.3 76.5 - - - +
334E TRP* 1.3 83.9 + - - +
335E PRO* 4.0 10.5 - - + +
352E HIS* 3.6 28.4 + + + -
353E ASP 3.4 8.1 + - - -
354E TYR* 3.2 47.7 + + + -
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Residues in contact with TRP 334 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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332E GLU* 3.2 46.0 - - + -
333E HIS* 1.3 82.4 - - - +
335E PRO* 1.3 80.6 - - + +
336E ASN* 5.9 0.2 - - + -
353E ASP* 2.9 49.2 + - + +
355E ARG* 3.3 48.2 - - - +
702E NAG 4.5 17.1 + - + +
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Residues in contact with PRO 335 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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307E SER* 6.2 0.7 - - - +
310E LEU* 3.6 43.3 - - + -
333E HIS* 4.0 4.9 - - + +
334E TRP* 1.3 100.4 - - + +
336E ASN* 1.3 67.4 + - - +
350E THR* 5.6 2.5 - - + -
351E VAL 3.5 7.4 - - - +
352E HIS* 3.5 28.0 - - + +
353E ASP* 5.9 0.4 - - - -
702E NAG 4.0 9.0 - - - +
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Residues in contact with ASN 336 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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294C ARG* 4.1 6.2 + - - -
334E TRP* 5.9 0.2 - - + -
335E PRO* 1.3 75.3 - - - +
337E GLU* 1.3 75.2 + - - +
338E THR* 6.1 1.3 - - - -
350E THR* 3.3 8.6 - - - +
351E VAL* 2.9 36.0 + - + +
353E ASP* 5.7 3.8 - - - +
702E NAG 1.4 73.2 + - - +
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Residues in contact with GLU 337 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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294C ARG* 3.2 31.3 + - + +
295C THR* 4.9 2.9 - - - -
296C ILE 5.3 1.6 - - - +
303E VAL* 3.8 27.3 - - - +
336E ASN* 1.3 89.6 + - - +
338E THR* 1.3 63.2 + - - +
348E ARG* 2.9 39.5 + - + +
349E ALA 3.2 13.9 - - - +
350E THR* 4.1 13.6 - - + +
351E VAL 4.6 0.4 - - - +
702E NAG 5.0 2.4 + - - +
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Residues in contact with THR 338 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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297E ARG* 6.1 0.2 - - - +
299E PHE* 5.6 4.3 - - + -
336E ASN* 6.1 1.1 - - - -
337E GLU* 1.3 74.8 - - - +
339E SER* 1.3 76.8 + - - +
340E VAL* 6.3 0.2 - - + -
348E ARG* 3.3 11.8 - - - +
349E ALA* 2.9 32.6 + - + +
351E VAL* 3.9 28.3 - - + -
702E NAG 4.6 14.6 + - - -
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Residues in contact with SER 339 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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338E THR* 1.3 92.7 + - - +
340E VAL* 1.3 60.6 + - - +
346E PHE* 3.9 34.7 - - - -
347E VAL 3.8 4.3 - - - -
348E ARG* 4.4 7.4 - - - +
349E ALA* 6.1 0.2 - - - -
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Residues in contact with VAL 340 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299E PHE* 4.6 27.8 - - + -
301E ALA* 6.6 0.2 - - + -
338E THR* 4.3 0.6 + - + -
339E SER* 1.3 75.2 - - - +
341E GLN* 1.3 78.0 + - - +
346E PHE* 3.4 4.3 - - - -
347E VAL* 2.9 49.2 + - + +
349E ALA* 4.7 8.5 - - + +
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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