Contacts of the strand formed by residues 306 - 309 (chain E) in PDB entry 3KQG
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 TRP 306 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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233E VAL* 3.7 15.9 - - + -
239E GLN* 3.3 23.3 + - - +
253E ILE* 3.4 22.7 - - + +
255E LEU* 3.6 24.7 - - + -
266E TRP* 3.6 32.1 - + - -
272E PHE* 4.4 1.1 - + - -
277E SER* 3.5 39.0 - - - -
280E PHE* 2.9 34.0 + + + +
281E TRP* 3.5 43.8 - + + -
282E ILE* 2.9 27.4 + - - +
285E GLU* 3.8 1.7 - - - +
297E ASN 3.3 6.3 - - - +
298E ILE* 3.9 11.7 - - + +
305E ALA* 1.3 78.7 - - - +
307E ASN* 1.3 58.5 + - - +
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Residues in contact with ASN 307 (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 TRP* 4.1 5.8 - - - -
282E ILE* 4.2 3.1 - - + -
285E GLU* 2.5 23.4 - - + +
293E GLU* 5.1 1.8 + - - -
296E GLY* 3.3 1.9 - - - -
297E ASN* 2.8 43.7 + - - +
299E LYS* 3.5 37.0 - - + +
305E ALA 3.7 0.4 + - - -
306E TRP* 1.3 73.8 - - - +
308E ASP* 1.3 72.7 + - - +
309E ALA* 4.5 7.5 - - - +
315E PHE* 6.3 0.4 - - - -
400E CA 2.4 23.9 - - - -
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Residues in contact with ASP 308 (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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257E LYS* 5.8 0.5 - - - -
264E TRP* 3.8 23.6 - - + -
281E TRP* 3.9 3.5 - - + -
285E GLU* 2.5 14.9 - - - +
286E PRO* 3.4 18.3 - - + +
287E ASN* 3.1 2.9 + - - +
288E ASN* 2.8 32.1 + - - +
293E GLU* 2.7 21.2 - - + +
295E CYS 3.2 9.9 - - - +
296E GLY* 4.2 1.6 - - - -
307E ASN* 1.3 78.1 + - - +
309E ALA* 1.3 58.4 + - - +
400E CA 2.4 49.2 - - - -
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Residues in contact with ALA 309 (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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252E TRP* 3.7 19.7 - - + -
293E GLU* 3.4 11.9 - - - +
295E CYS* 2.7 28.1 + - - +
297E ASN* 3.8 17.9 - - - +
307E ASN* 4.0 5.6 + - - +
308E ASP* 1.3 74.6 - - - +
310E PRO* 1.3 76.8 - - + +
311E CYS 3.3 0.2 + - - -
313E LYS* 4.9 0.2 - - + -
315E PHE* 4.1 11.4 - - + -
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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