Contacts of the strand formed by residues 355 - 360 (chain B) in PDB entry 3P3W
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 ILE 355 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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115B PRO* 5.1 3.1 - - + -
116B ALA 4.1 9.6 - - - +
117B LEU* 4.5 10.1 - - + -
120B ALA* 3.9 22.2 - - + -
222B LEU* 5.0 2.0 - - + -
242B PHE* 4.4 20.2 - - + -
243B GLN 3.6 19.3 - - - +
244B ILE* 5.0 10.3 - - + +
353B TYR* 3.6 35.9 - - + -
354B THR* 1.3 71.4 - - - +
356B ASP* 1.3 72.1 + - - +
357B VAL* 3.4 4.3 + - + +
370B TYR* 3.4 1.3 - - - -
371B TRP* 2.8 51.8 + - + +
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Residues in contact with ASP 356 (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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242B PHE* 4.0 2.1 - - - -
243B GLN 2.9 36.1 + - - +
244B ILE 3.9 6.8 - - - +
245B VAL 3.6 11.4 - - - +
246B ASN* 3.4 36.6 + - - +
354B THR* 3.9 15.7 + - - +
355B ILE* 1.3 72.4 - - - +
357B VAL* 1.3 61.6 + - - +
358B TYR* 3.6 24.6 + - + +
369B GLY 3.8 5.1 - - - +
370B TYR* 4.7 5.0 - - - +
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Residues in contact with VAL 357 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120B ALA* 6.2 0.2 - - + -
124B LEU* 3.9 29.2 - - + -
240B THR* 4.1 13.2 - - + -
241B GLY 3.9 9.9 - - - +
242B PHE* 5.0 6.7 - - + +
355B ILE* 3.8 12.3 - - + +
356B ASP* 1.3 73.1 - - - +
358B TYR* 1.3 56.8 + - - +
367B LYS* 3.6 5.9 - - - +
368B ALA* 2.7 36.4 + - + -
369B GLY 2.7 24.7 + - - +
371B TRP* 4.4 9.2 - - + -
377B PHE* 3.9 32.1 - - + -
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Residues in contact with TYR 358 (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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224B PHE* 4.1 21.9 - + + -
239B ILE 3.7 1.0 - - - +
240B THR* 3.5 5.9 - - - +
241B GLY 2.9 35.6 + - - +
243B GLN* 3.5 48.6 + - + -
245B VAL 3.8 14.9 + - - -
246B ASN* 4.3 11.1 + - - -
247B ASN* 5.0 3.6 + - - +
356B ASP* 3.6 27.3 - - + +
357B VAL* 1.3 73.4 - - - +
359B GLU* 1.3 61.7 + - - +
360B MET* 4.0 3.1 + - + -
366B ARG 3.7 7.2 - - - +
367B LYS* 3.9 28.9 - - + -
368B ALA* 4.5 0.2 - - - -
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Residues in contact with GLU 359 (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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127B TYR* 4.6 8.1 + - - -
128B TYR* 2.7 37.3 + - - +
239B ILE 3.6 3.1 - - - +
240B THR* 4.2 6.7 - - + +
358B TYR* 1.3 73.0 - - - +
360B MET* 1.3 60.8 + - - +
361B LYS* 3.2 37.0 + - + +
364B GLY 4.0 1.6 - - - +
365B SER* 3.8 1.7 - - - -
366B ARG* 3.0 57.2 + - - +
368B ALA* 3.6 26.6 - - + +
377B PHE* 5.1 1.9 - - - -
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Residues in contact with MET 360 (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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224B PHE* 3.6 21.1 - - + -
229B LEU* 3.5 33.7 - - + -
233B MET* 3.7 40.8 - - + +
237B ALA 3.5 4.2 - - - +
239B ILE* 2.7 51.7 + - + +
358B TYR* 5.2 2.5 - - + -
359B GLU* 1.3 75.0 - - - +
361B LYS* 1.3 58.6 + - - +
364B GLY 4.2 1.3 - - - -
365B SER* 4.4 14.6 - - - +
366B ARG 5.2 1.6 - - - +
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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