Contacts of the strand formed by residues 388 - 397 (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 VAL 388 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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270E PRO* 5.3 0.4 - - - -
375E LEU* 3.7 33.2 - - + -
376E VAL 3.4 6.7 - - - +
377E ASN* 3.8 20.4 - - - +
387E GLY* 1.3 84.3 + - - +
389E LEU* 1.3 66.4 + - - +
703E NAG 4.5 15.3 - - - +
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Residues in contact with LEU 389 (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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270E PRO* 4.0 31.4 - - + +
271E THR* 4.5 1.8 - - - +
272E PHE* 3.6 46.0 - - + +
298E VAL* 3.7 33.2 - - + -
375E LEU* 3.4 10.6 - - - +
376E VAL* 2.9 42.2 + - + +
388E VAL* 1.3 76.2 - - - +
390E LEU* 1.3 65.4 + - - +
391E LEU* 5.1 1.6 - - + -
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Residues in contact with LEU 390 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272E PHE* 3.2 24.6 - - - -
277E ASP* 5.0 1.7 - - - +
319E LEU* 4.1 25.8 - - + -
373E ALA* 4.2 5.2 - - + -
374E VAL 3.6 15.7 - - - +
375E LEU* 4.1 14.6 - - + -
389E LEU* 1.3 79.0 - - - +
391E LEU* 1.3 71.4 + - - +
392E HIS* 4.1 28.0 - - + +
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Residues in contact with LEU 391 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272E PHE* 3.6 30.5 - - + -
277E ASP 4.4 2.7 - - - -
296E LEU* 3.7 29.4 - - + -
297E ARG 5.3 0.2 - - - +
298E VAL* 4.3 11.0 - - + -
354E TYR* 3.8 39.9 - - + -
373E ALA* 3.3 7.3 - - - +
374E VAL* 2.8 48.7 + - + +
376E VAL* 4.2 14.1 - - + -
389E LEU* 5.1 1.1 - - + -
390E LEU* 1.3 77.0 - - - +
392E HIS* 1.3 65.8 + - - +
393E PHE* 4.7 8.7 - - + -
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Residues in contact with HIS 392 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277E ASP* 3.3 30.2 + - + -
278E THR* 3.4 25.3 - - + +
279E ALA 3.9 7.6 + - - -
296E LEU* 3.8 12.5 - - - +
371E GLN* 4.2 21.2 + - + +
372E LEU 3.5 7.8 + - - +
373E ALA* 4.6 8.5 - - + +
390E LEU* 4.1 29.4 - - + +
391E LEU* 1.3 77.7 + - - +
393E PHE* 1.3 75.3 + - - +
394E ASN* 5.8 1.3 - - - +
704E NAG 6.3 0.4 - - - -
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Residues in contact with PHE 393 (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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278E THR* 5.1 0.2 - - - -
279E ALA 3.5 7.0 - - - -
294E ALA* 3.6 41.3 - - + -
296E LEU* 3.6 28.0 - - + -
331E VAL* 5.6 2.0 - - + -
354E TYR* 4.6 11.4 - - + -
355E ARG* 4.7 1.8 - - - -
356E LEU* 3.5 41.7 - - + -
370E MET 3.8 0.3 - - - +
371E GLN* 3.4 5.9 - - - +
372E LEU* 2.9 43.2 + - + +
374E VAL* 3.7 33.9 - - + -
391E LEU* 4.7 8.5 - - + -
392E HIS* 1.3 85.9 - - - +
394E ASN* 1.3 64.2 + - - +
395E VAL* 4.0 3.8 + - + -
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Residues in contact with ASN 394 (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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278E THR* 4.2 3.6 - - - +
279E ALA 3.6 6.7 + - - -
280E SER* 3.3 12.2 - - - -
281E ALA 3.0 27.0 + - - +
370E MET 3.5 6.1 - - - +
371E GLN* 4.1 15.8 - - - +
392E HIS* 5.8 1.2 - - - +
393E PHE* 1.3 77.0 - - - +
395E VAL* 1.3 62.9 + - - +
396E SER* 4.2 1.3 - - - +
704E NAG 1.4 69.5 + - - +
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Residues in contact with VAL 395 (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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281E ALA 3.3 10.8 - - - +
283E VAL* 3.8 27.6 - - + -
293E VAL* 3.8 19.5 - - + -
294E ALA* 5.6 0.7 - - + -
329E PHE* 4.0 19.5 - - + -
356E LEU* 4.1 19.5 - - + -
369E THR* 3.7 0.7 - - - -
370E MET* 2.8 46.2 + - + +
372E LEU* 5.1 5.6 - - + -
393E PHE* 4.0 6.7 + - + -
394E ASN* 1.3 78.6 - - - +
396E SER* 1.3 66.2 + - - +
397E VAL* 4.1 5.0 + - + -
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Residues in contact with SER 396 (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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281E ALA 3.8 4.9 + - - -
282E VAL* 3.3 26.0 - - - +
283E VAL 3.2 19.8 + - - -
368E ARG 3.5 10.3 - - - -
369E THR* 3.2 21.4 + - - +
394E ASN* 4.2 1.8 - - - +
395E VAL* 1.3 71.8 + - - +
397E VAL* 1.3 62.1 + - - +
398E LEU* 3.3 8.7 + - - -
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Residues in contact with VAL 397 (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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283E VAL* 3.5 30.7 - - + +
287E ARG* 5.1 4.9 - - - +
324E TRP* 3.6 28.9 - - + -
329E PHE* 5.0 4.3 - - + -
362E LEU* 4.0 22.9 - - + -
366E GLU* 4.5 5.6 - - + +
367E ASN* 3.4 8.6 - - - +
368E ARG* 2.9 52.5 + - + +
370E MET* 5.1 3.6 - - - -
395E VAL* 4.0 7.6 - - + -
396E SER* 1.3 68.3 - - - +
398E LEU* 1.3 65.7 + - - +
399E PRO* 4.0 0.2 - - - +
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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