Contacts of the strand formed by residues 330 - 335 (chain B) in PDB entry 4DTY
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 330 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26B VAL* 4.9 11.7 - - + -
29B LEU* 6.4 0.9 - - + -
51B TYR* 5.7 3.8 - - + -
328B ALA* 3.3 5.6 + - - +
329B PRO* 1.3 82.2 - - - +
331B PHE* 1.3 64.9 + - - +
354B MET* 3.8 17.5 - - + -
355B VAL 3.2 11.7 - - - +
356B LEU* 4.7 13.2 - - + -
357B ILE* 4.7 0.4 - - - -
501B HEM 5.4 1.9 - - - +
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Residues in contact with PHE 331 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62B CYS* 4.6 3.4 - - - -
72B SER* 6.1 0.7 - - - -
330B ALA* 1.3 75.1 - - - +
332B SER* 1.3 63.0 + - - +
333B LEU* 4.3 21.5 - - + -
354B MET* 3.3 6.3 - - - +
355B VAL* 2.9 64.8 + - + +
357B ILE* 3.7 31.4 - - + -
391B LYS* 4.4 13.2 - - + -
394B GLY* 3.8 24.2 - - - -
395B ASN* 4.2 22.4 - - + -
501B HEM 3.3 39.0 - - + +
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Residues in contact with SER 332 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69B LYS* 3.7 6.6 - - - +
70B ASN* 2.9 57.1 + - - +
72B SER* 3.9 14.8 - - - -
331B PHE* 1.3 76.0 - - - +
333B LEU* 1.3 70.2 + - - +
352B GLU* 4.5 3.8 + - - +
353B LEU 3.2 12.1 + - - -
354B MET* 3.4 20.3 - - - -
501B HEM 5.0 2.3 + - - +
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Residues in contact with LEU 333 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61B ALA* 3.6 43.1 - - + +
62B CYS* 5.4 0.9 - - - -
67B PHE* 4.2 13.0 - - + +
68B ASP* 3.1 24.7 - - - +
69B LYS* 4.1 4.3 - - + +
70B ASN* 3.6 7.0 - - - +
331B PHE* 4.3 18.8 - - + -
332B SER* 1.3 78.6 - - - +
334B TYR* 1.3 62.4 + - - +
352B GLU* 3.3 7.3 - - - +
353B LEU* 2.9 39.3 + - + +
355B VAL* 3.9 20.2 - - + -
395B ASN* 5.7 7.2 - - + +
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Residues in contact with TYR 334 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67B PHE* 3.2 9.4 - - - -
68B ASP* 2.7 64.6 + - + +
69B LYS 3.2 28.9 - - - -
70B ASN* 4.0 14.6 - - + +
90B TRP* 4.5 12.6 - + - -
92B HIS* 4.3 13.4 - + - -
333B LEU* 1.3 75.6 - - - +
335B ALA* 1.3 75.7 + - - +
336B LYS* 4.2 16.3 + - + +
350B GLY* 3.9 17.3 - - - +
351B ASP 3.3 9.6 - - - +
352B GLU* 4.6 4.0 - - + -
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Residues in contact with ALA 335 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66B ARG 3.7 0.7 - - - -
67B PHE* 3.7 24.5 - - + -
334B TYR* 1.3 76.5 - - - +
336B LYS* 1.3 64.6 + - - +
337B GLU 3.6 14.8 - - - +
339B THR* 4.7 0.9 - - + -
347B LEU* 4.5 11.0 - - + -
348B GLU 3.6 24.0 - - - +
349B LYS* 4.1 0.7 - - - +
350B GLY 2.9 24.7 + - - +
351B ASP 2.9 15.1 + - - +
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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
------------------------------------------------------------
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