Contacts of the helix formed by residues 348 - 357 (chain T) in PDB entry 2P8W
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 ALA 348 (chain T).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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123T ASP* 4.2 24.9 - - + +
343T PRO* 6.3 0.4 - - + -
344T SER 4.7 5.8 - - - +
345T PRO* 3.4 10.9 + - + +
347T THR* 1.3 76.5 - - - +
349T GLN* 1.3 60.4 + - + +
350T ALA 2.9 9.9 + - - -
351T TYR* 3.0 40.1 + - + +
352T ARG* 3.1 24.0 + - - +
399T ARG* 5.3 1.3 - - - +
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Residues in contact with GLN 349 (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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345T PRO* 2.8 31.1 + - - +
348T ALA* 1.3 71.0 - - - +
350T ALA* 1.3 60.9 + - - +
351T TYR 3.3 0.2 - - - -
352T ARG* 3.8 8.5 - - - +
353T ALA* 3.2 26.1 + - - +
356T LEU* 5.5 1.1 - - + -
369T ILE* 2.9 26.7 + - + +
370T LYS* 3.3 8.6 - - - +
372T CYS* 3.5 19.5 - - + +
399T ARG* 2.9 32.5 + - - +
401T PHE* 3.1 49.1 + - + -
451T GLY* 4.1 2.9 - - - -
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Residues in contact with ALA 350 (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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346T VAL 3.8 10.8 + - - +
347T THR* 3.4 15.2 + - - +
348T ALA 2.9 0.8 + - - -
349T GLN* 1.3 79.3 - - - +
351T TYR* 1.3 61.2 + - + +
353T ALA* 4.7 1.2 - - - +
370T LYS* 3.6 36.0 + - + +
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Residues in contact with TYR 351 (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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123T ASP* 6.1 0.3 - - - +
150T ARG* 3.3 54.7 + - + +
196T VAL* 6.2 2.9 - - + -
197T LEU* 5.6 7.9 - - + -
343T PRO* 5.1 12.8 - - - +
347T THR* 3.5 30.7 - - + +
348T ALA* 3.5 26.3 + - - +
350T ALA* 1.3 79.2 - - + +
352T ARG* 1.3 74.5 + - - +
353T ALA 3.6 0.7 - - - -
354T GLU* 5.3 2.6 + - - +
355T GLN* 5.3 3.1 - - - +
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Residues in contact with ARG 352 (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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120T ARG* 3.2 26.5 + - - +
122T THR 5.1 2.2 - - - -
123T ASP* 4.5 11.6 + - - -
149T GLU* 4.0 36.6 + - - +
150T ARG* 4.6 7.9 - - - -
348T ALA* 3.1 22.1 + - - +
349T GLN* 4.3 2.4 - - - +
351T TYR* 1.3 98.1 - - + +
353T ALA* 1.3 67.0 + - - +
354T GLU 3.4 2.5 - - - -
355T GLN* 3.2 21.8 + - + +
356T LEU* 3.1 50.6 + - + +
399T ARG* 3.6 21.8 - - - +
401T PHE* 4.0 16.2 - - - -
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Residues in contact with ALA 353 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
349T GLN 3.2 14.9 + - - +
350T ALA 4.7 1.8 - - - +
351T TYR 3.6 0.6 - - - -
352T ARG* 1.3 77.4 - - - +
354T GLU* 1.3 57.6 + - - +
356T LEU* 3.3 2.4 + - - +
357T TYR* 2.9 32.6 + - - +
366T CYS* 4.0 7.0 - - - +
369T ILE* 3.9 16.4 - - + +
370T LYS* 3.1 46.4 - - + +
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Residues in contact with GLU 354 (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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351T TYR 5.3 2.3 + - - +
352T ARG 3.4 1.0 - - - -
353T ALA* 1.3 74.0 - - - +
355T GLN* 1.3 59.1 + - + +
357T TYR 2.8 25.2 - - - +
361T ALA* 3.1 31.9 - - + +
366T CYS* 4.3 7.2 - - - -
370T LYS* 3.4 31.3 + - - +
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Residues in contact with GLN 355 (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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148T GLY 4.4 15.0 + - - +
149T GLU* 5.4 2.3 - - - -
150T ARG* 4.1 38.5 + - - +
194T ASP* 4.5 6.5 + - - -
351T TYR 5.3 2.2 + - - +
352T ARG* 3.2 19.8 + - + +
354T GLU* 1.3 78.5 - - + +
356T LEU* 1.3 67.3 + - + +
357T TYR 3.1 5.0 + - - +
358T GLU* 4.9 1.0 - - - +
479T LYS* 3.8 40.1 + - + +
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Residues in contact with LEU 356 (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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120T ARG* 4.3 23.3 - - - +
349T GLN* 5.5 2.2 - - + -
352T ARG* 3.1 58.9 + - + +
353T ALA* 3.7 6.5 - - - +
355T GLN* 1.3 80.9 - - + +
357T TYR* 1.3 57.6 + - - +
369T ILE* 4.6 3.8 - - + -
381T TYR* 6.4 1.1 - - + -
401T PHE* 3.5 39.3 - - + -
478T MET* 3.1 50.5 - - + +
479T LYS* 3.6 6.9 + - + +
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Residues in contact with TYR 357 (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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353T ALA 2.9 16.9 + - - +
354T GLU* 2.8 19.7 - - - +
355T GLN 4.0 2.4 - - - +
356T LEU* 1.3 78.4 - - + +
358T GLU* 1.3 63.6 + - - +
359T GLY* 3.3 32.0 - - - +
360T PRO 3.8 0.2 - - - -
363T ASP* 3.1 38.7 + - + -
365T ASN* 3.6 8.7 + - + +
366T CYS* 3.5 30.1 - - + -
369T ILE* 5.1 6.5 - - + -
379T MET* 3.3 23.8 - - + -
474T THR 4.5 0.5 + - - -
475T ALA 3.8 0.2 - - - -
476T HIS* 2.8 56.3 + - + +
477T ASN 4.3 2.9 - - - -
478T MET* 4.5 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