Contacts of the strand formed by residues 278 - 283 (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 THR 278 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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276E VAL* 3.5 15.0 + - - +
277E ASP* 1.3 96.5 + - - +
279E ALA* 1.3 68.3 + - - +
296E LEU* 4.0 3.1 - - - +
392E HIS* 3.4 29.6 - - + +
394E ASN* 4.2 9.9 - - - +
704E NAG 3.6 44.2 - - + +
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Residues in contact with ALA 279 (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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276E VAL* 5.9 2.2 - - + -
278E THR* 1.3 75.4 - - - +
280E SER* 1.3 61.2 + - - +
294E ALA* 4.2 13.2 - - + +
295E THR 3.8 13.9 - - - +
296E LEU* 3.7 27.3 - - + +
392E HIS 3.9 0.6 + - - -
393E PHE* 3.5 30.0 - - - -
394E ASN 3.6 1.2 + - - +
704E NAG 5.2 0.2 - - - -
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Residues in contact with SER 280 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278E THR 4.4 0.2 + - - -
279E ALA* 1.3 77.4 - - - +
281E ALA* 1.3 64.3 + - - +
282E VAL* 5.9 0.7 - - - -
294E ALA* 4.8 1.3 - - - +
394E ASN* 3.3 22.7 - - - -
704E NAG 3.5 35.2 + - - +
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Residues in contact with ALA 281 (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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280E SER* 1.3 76.3 - - - +
282E VAL* 1.3 66.5 + - - +
283E VAL 3.9 1.3 + - - -
293E VAL* 3.3 41.3 - - + +
294E ALA* 4.1 5.0 - - + +
394E ASN 3.0 16.9 + - - +
395E VAL* 3.3 19.1 - - - +
396E SER 3.8 0.3 + - - -
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Residues in contact with VAL 282 (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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280E SER* 5.9 0.4 - - - -
281E ALA* 1.3 76.6 - - - +
283E VAL* 1.3 62.3 + - - +
284E GLU* 3.2 16.5 + - + +
396E SER* 3.3 29.4 - - - +
398E LEU* 3.8 30.3 - - + -
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Residues in contact with VAL 283 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281E ALA 3.9 0.4 + - - -
282E VAL* 1.3 69.6 - - - +
284E GLU* 1.3 59.0 + - - +
286E LYS* 5.4 2.5 - - + +
287E ARG* 4.2 22.7 + - + +
293E VAL* 4.1 28.3 - - + -
329E PHE* 4.7 5.2 - - + -
358E LEU* 4.6 11.0 - - + -
362E LEU* 4.3 14.4 - - + -
395E VAL* 3.8 22.7 - - + -
396E SER 3.2 5.8 + - - -
397E VAL* 3.5 21.7 - - + -
398E LEU 3.4 24.1 + - - +
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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