Contacts of the strand formed by residues 315 - 321 (chain T) in PDB entry 6O81
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 PHE 315 (chain T).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200M GLY 4.1 2.8 + - - +
201M TYR* 3.1 52.8 - + + +
293T GLU* 5.5 5.8 - - + -
294T ILE 3.4 18.4 - - - +
295T GLU* 3.7 24.5 - - + -
313T PRO* 3.6 30.7 - - + -
314T LYS* 1.3 72.9 - - - +
316T SER* 1.3 60.8 + - - +
362T GLY* 6.0 2.5 - - - -
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Residues in contact with SER 316 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201M TYR* 4.3 6.3 - - - -
293T GLU* 4.5 2.2 - - - -
294T ILE* 2.9 34.3 + - - +
314T LYS* 3.9 4.1 + - - -
315T PHE* 1.3 75.8 - - - +
317T LYS* 1.3 62.2 + - - +
341T THR* 4.0 12.8 - - - -
342T LYS 3.8 27.1 - - - -
343T ILE* 4.2 11.0 - - - -
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Residues in contact with LYS 317 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201M TYR* 4.9 15.7 + - + -
291T GLY* 4.5 13.7 - - - +
292T GLN 3.9 4.9 - - - -
293T GLU* 4.1 7.8 - - + +
316T SER* 1.3 72.3 - - - +
318T ILE* 1.3 61.1 + - - +
319T VAL* 3.1 5.2 + - - +
341T THR* 3.4 0.6 - - - -
342T LYS* 3.0 34.6 + - + +
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Residues in contact with ILE 318 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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289T LYS 4.3 14.1 - - - +
290T VAL* 3.7 2.9 - - - -
291T GLY* 2.7 32.2 + - - -
292T GLN* 3.0 21.4 + - + +
294T ILE* 5.2 7.0 - - + -
316T SER 3.5 2.2 + - - +
317T LYS* 1.3 68.2 - - - +
319T VAL* 1.3 63.5 + - - +
320T SER 4.9 7.2 - - - +
339T VAL* 5.4 8.5 - - + -
340T GLY 4.5 0.2 - - - -
341T THR* 4.0 11.0 - - - +
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Residues in contact with VAL 319 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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290T VAL* 4.1 9.9 - - - +
291T GLY 5.0 0.2 + - - -
317T LYS* 3.1 8.4 + - - +
318T ILE* 1.3 74.6 - - - +
320T SER* 1.3 65.2 + - - +
340T GLY 3.1 14.4 + - - +
341T THR 4.4 8.1 - - - +
342T LYS* 4.7 4.0 - - + +
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Residues in contact with SER 320 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290T VAL* 4.7 7.4 - - - -
318T ILE* 3.5 5.4 - - - +
319T VAL* 1.3 82.0 + - - +
321T LEU* 1.3 61.8 + - - +
322T PHE* 3.8 7.9 - - - -
339T VAL* 3.5 5.2 - - - +
340T GLY* 2.9 33.5 + - - +
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Residues in contact with LEU 321 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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288T LEU* 5.4 1.1 - - + +
289T LYS 6.1 0.7 - - - -
290T VAL* 5.0 4.8 - - + +
320T SER* 1.3 73.7 - - - +
322T PHE* 1.3 58.2 + - - +
323T ALA 3.8 0.2 - - - -
327T ASP* 3.3 26.3 - - + +
328T LEU 3.8 18.3 + - - +
329T GLN* 4.2 12.5 - - - +
331T ALA* 4.4 18.2 - - + -
338T GLY 3.2 9.9 - - - +
339T VAL* 4.4 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