Contacts of the strand formed by residues 292 - 300 (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 292 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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291E THR* 1.3 80.2 - - - +
293E VAL* 1.3 68.2 + - - +
294E ALA 4.6 0.4 - - - +
295E THR* 3.8 22.2 - - - +
355E ARG* 4.1 33.2 - - + +
356E LEU 3.7 5.8 - - - +
357E VAL* 4.9 5.2 - - + -
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Residues in contact with VAL 293 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281E ALA* 3.3 33.8 - - + +
283E VAL* 4.1 20.9 - - + -
291E THR* 3.6 15.0 - - + +
292E VAL* 1.3 77.5 - - - +
294E ALA* 1.3 62.3 + - + +
329E PHE* 4.1 21.3 - - + -
356E LEU* 3.0 21.6 + - + +
358E LEU* 4.4 9.4 - - + -
395E VAL* 3.8 24.9 - - + -
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Residues in contact with ALA 294 (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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279E ALA* 4.2 17.5 - - + +
280E SER 4.8 0.7 - - - +
281E ALA* 4.1 14.6 - - + +
292E VAL* 5.2 0.2 - - - -
293E VAL* 1.3 85.4 - - + +
295E THR* 1.3 65.4 + - - +
355E ARG* 3.3 5.0 - - - +
356E LEU* 3.2 24.8 + - - +
393E PHE* 3.6 28.5 - - + -
395E VAL* 5.6 1.1 - - + -
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Residues in contact with THR 295 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279E ALA* 3.8 9.7 - - - +
292E VAL* 3.8 19.1 - - - +
294E ALA* 1.3 81.1 + - - +
296E LEU* 1.3 79.3 + - - +
297E ARG* 5.2 3.8 - - + -
353E ASP* 5.0 5.6 - - + +
354E TYR 3.3 12.1 - - - +
355E ARG* 3.8 26.0 + - - +
393E PHE* 4.1 0.6 - - - -
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Residues in contact with LEU 296 (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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272E PHE* 5.3 0.2 - - + -
276E VAL* 3.7 27.1 - - + +
277E ASP 3.9 19.3 - - - +
278E THR 4.0 2.2 - - - +
279E ALA* 3.7 22.4 - - + +
295E THR* 1.3 78.8 - - - +
297E ARG* 1.3 67.2 + - - +
353E ASP* 3.6 3.8 - - - -
354E TYR* 2.9 34.6 + - - +
391E LEU* 3.7 37.9 - - + -
392E HIS 3.8 4.7 - - - +
393E PHE* 3.6 31.2 - - + -
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Residues in contact with ARG 297 (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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272E PHE* 4.5 5.4 - - - -
273E PRO* 3.3 36.8 - - + +
276E VAL 5.3 1.7 - - - +
295E THR* 5.2 5.2 - - + -
296E LEU* 1.3 79.3 - - - +
298E VAL* 1.3 67.8 + - - +
351E VAL* 3.4 35.1 - - + +
352E HIS 3.2 6.3 - - - +
353E ASP* 3.3 19.3 + - - +
391E LEU* 5.3 0.3 - - - +
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Residues in contact with VAL 298 (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* 3.7 30.1 - - + -
271E THR 4.3 3.1 - - - +
272E PHE* 5.0 0.9 - - + +
273E PRO* 4.6 1.3 - - - -
297E ARG* 1.3 80.5 - - - +
299E PHE* 1.3 64.4 + - - +
351E VAL* 3.4 7.3 - - - +
352E HIS* 2.9 50.0 + - + -
354E TYR* 3.7 26.5 - - + -
376E VAL* 4.8 8.3 - - + -
389E LEU* 3.7 21.8 - - + -
391E LEU* 4.3 15.0 - - + -
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Residues in contact with PHE 299 (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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269E ALA 4.4 0.5 - - - +
270E PRO* 3.4 2.9 - - - +
271E THR* 2.8 51.9 + - - +
272E PHE 4.8 7.2 - - - +
273E PRO* 4.7 8.2 - - + +
298E VAL* 1.3 74.6 - - - +
300E ASP* 1.3 69.1 + - - +
301E ALA* 4.5 10.3 - - + -
338E THR* 5.6 4.0 - - + -
340E VAL* 4.6 24.2 - - + -
349E ALA* 3.9 27.1 - - + -
350E THR 3.8 1.3 - - - -
351E VAL* 4.0 23.3 - - + -
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Residues in contact with ASP 300 (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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268E SER 3.0 10.4 - - - +
269E ALA 4.4 1.7 - - - +
270E PRO* 4.5 8.1 - - + -
298E VAL 4.2 0.2 + - - -
299E PHE* 1.3 78.7 - - - +
301E ALA* 1.3 64.9 + - - +
302E ASP* 2.9 16.2 + - - +
314E TYR* 3.8 10.6 + - - -
349E ALA* 3.3 4.4 - - - +
350E THR* 2.9 47.7 + - - +
352E HIS* 3.9 12.3 + - + +
378E ASP* 2.2 30.2 - - - +
708E CA 2.3 20.1 - - - -
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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