Contacts of the strand formed by residues 351 - 355 (chain E) in PDB entry 3SWD
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 351 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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348A GLU* 4.1 17.3 + - + +
349A SER* 5.9 0.9 - - - -
353A ILE* 5.2 1.8 - - + -
322E PHE* 3.9 26.9 - - + -
323E ILE 3.4 6.5 - - - +
324E THR* 2.8 29.4 + - - +
332E PHE* 4.7 2.2 - - - -
346E GLU 4.0 0.2 - - - +
347E ILE* 3.5 3.4 - - - +
348E GLU* 2.9 37.9 + - - +
349E SER 3.4 1.2 + - - -
350E ASN* 1.3 85.1 + - - +
352E VAL* 1.3 66.1 + - - +
353E ILE* 4.0 9.0 + - + +
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Residues in contact with VAL 352 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311E THR* 4.3 15.9 - - + +
321E GLY 4.0 0.3 - - - +
322E PHE* 3.4 5.0 - - - +
323E ILE* 2.9 52.1 + - + +
332E PHE* 4.0 23.2 - - + -
335E VAL* 4.0 19.3 - - + -
345E ALA* 4.1 12.8 - - + -
346E GLU 3.5 9.9 - - - +
347E ILE* 4.4 7.9 - - + +
351E THR* 1.3 74.4 - - - +
353E ILE* 1.3 62.9 + - - +
354E CYS* 3.8 16.1 + - - -
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Residues in contact with ILE 353 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320A THR* 6.1 0.9 - - + -
322A PHE* 3.7 40.2 - - + -
351A THR* 4.7 6.5 - - + -
353A ILE* 5.0 13.9 - - + -
320E THR* 4.2 10.3 - - + -
321E GLY 4.0 2.7 - - - +
322E PHE* 4.4 8.1 - - + -
345E ALA* 3.3 5.9 - - - -
346E GLU* 2.8 41.0 + - + +
348E GLU* 4.1 22.4 - - + -
351E THR* 4.3 13.9 - - + +
352E VAL* 1.3 76.3 - - - +
354E CYS* 1.3 61.0 + - - +
355E HIS* 3.9 27.3 + - + +
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Residues in contact with CYS 354 (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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311E THR* 4.2 13.7 - - - -
314E ASN* 3.6 33.9 - - + -
315E LEU* 3.7 20.4 - - + -
319E GLY 3.9 0.3 - - - +
320E THR* 3.1 11.3 - - - +
321E GLY 2.8 42.5 + - - +
323E ILE* 5.2 0.9 - - - -
344E HIS 4.0 2.9 - - - -
352E VAL* 4.0 25.4 - - - -
353E ILE* 1.3 75.4 - - - +
355E HIS* 1.3 63.3 + - - +
356E GLY 3.9 0.7 - - - -
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Residues in contact with HIS 355 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293A ASN* 5.1 5.8 + - - -
320A THR* 4.8 15.2 - - + -
321A GLY* 6.3 0.4 - - - -
322A PHE* 5.5 2.7 - + - -
314E ASN 4.6 0.9 - - - -
315E LEU* 4.2 3.3 - - - +
319E GLY 4.0 3.4 - - - -
320E THR* 3.1 36.1 + - + +
344E HIS* 3.0 48.0 + - + +
346E GLU* 2.5 35.1 + - - -
353E ILE* 3.9 12.3 - - + +
354E CYS* 1.3 72.5 - - - +
356E GLY* 1.3 65.3 + - - +
357E VAL* 3.6 4.9 + - - +
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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