Contacts of the strand formed by residues 297 - 300 (chain K) in PDB entry 6LTJ
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 297 (chain K).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151K ILE* 3.5 27.8 - - + -
293K LEU 3.8 6.1 - - - +
294K TYR* 4.0 9.4 - - + +
296K ASN* 1.3 77.4 - - - +
298K VAL* 1.3 61.9 + - - +
299K LEU* 5.3 5.5 - - - +
313K MET* 6.6 0.4 - - - -
317K ILE* 5.9 3.4 - - + -
327K ILE* 5.1 1.3 - - + -
328K LYS 3.3 14.1 + - - +
329K ILE* 3.2 38.6 - - + +
330K ILE* 3.1 26.1 + - - +
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Residues in contact with VAL 298 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141K SER* 5.1 3.6 - - - +
142K LEU* 3.7 30.1 - - + +
145K SER* 4.1 19.1 - - - -
147K ARG* 5.0 2.0 - - - -
151K ILE 2.9 13.9 + - - +
152K VAL* 3.4 16.8 - - + +
153K MET* 2.9 25.6 + - - +
296K ASN 5.4 0.9 - - - +
297K THR* 1.3 77.2 - - - +
299K LEU* 1.3 68.4 + - - +
300K SER* 6.1 0.2 - - - -
330K ILE* 3.3 34.3 - - + +
332K PRO* 5.1 5.6 - - + -
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Residues in contact with LEU 299 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153K MET* 3.7 27.4 - - + -
297K THR* 5.3 4.7 - - - +
298K VAL* 1.3 79.8 - - - +
300K SER* 1.3 62.5 + - - +
304K THR* 3.7 17.3 - - + -
309K ILE* 3.7 35.9 - - + +
310K ALA* 5.1 3.8 - - - -
313K MET* 4.4 27.6 - - + -
329K ILE* 5.2 11.0 - - + -
330K ILE 3.8 4.8 + - - -
331K ALA* 3.7 26.9 - - + +
332K PRO* 3.8 10.4 - - - +
335K ARG* 3.7 13.8 - - - +
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Residues in contact with SER 300 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141K SER* 3.9 27.1 + - - -
152K VAL* 3.6 12.2 - - - +
153K MET 2.7 22.3 + - - +
154K ASP* 3.3 16.2 + - - +
155K SER* 2.6 35.5 + - - -
298K VAL* 6.1 0.4 - - - -
299K LEU* 1.3 78.4 - - - +
301K GLY* 1.3 52.5 + - - +
304K THR* 3.1 6.2 + - - -
335K ARG* 3.9 5.6 - - - -
338K SER* 4.4 6.3 - - - -
339K VAL* 4.9 4.7 - - - -
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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