Contacts of the strand formed by residues 358 - 365 (chain B) in PDB entry 3SAJ
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 358 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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217B PHE* 5.7 2.2 - - + -
218B MET* 3.5 39.9 - - + -
222B LEU* 5.6 7.6 - - + -
226B LYS* 5.4 11.2 - - + -
351B ILE* 4.5 7.6 - - + -
352B GLU 4.4 2.2 - - - -
353B MET* 4.3 22.7 - - + +
356B ASP* 3.8 9.8 + - - +
357B GLY* 1.3 79.4 - - - +
359B ARG* 1.3 59.8 + - - +
360B LYS 4.0 1.2 + - - -
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Residues in contact with ARG 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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351B ILE* 4.1 3.7 - - - -
352B GLU* 3.3 36.8 + - + +
354B LYS* 3.1 38.5 - - + +
357B GLY* 3.5 9.5 + - - +
358B ILE* 1.3 73.8 - - - +
360B LYS* 1.3 65.5 + - - +
361B ILE* 3.1 9.8 + - - +
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Residues in contact with LYS 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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239B ASN* 5.9 1.6 - - - +
349B HIS* 2.5 46.2 + - + -
350B VAL 4.0 10.8 - - - +
351B ILE* 4.3 13.4 - - + +
358B ILE 4.0 1.8 + - - -
359B ARG* 1.3 75.0 - - - +
361B ILE* 1.3 65.6 + - - +
362B GLY* 3.3 24.2 + - - +
363B TYR* 4.0 12.3 - - - +
373B ALA* 4.2 12.3 - - - +
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Residues in contact with ILE 361 (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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121B HIS* 4.5 13.9 - - + +
122B TYR* 5.4 0.9 - - - +
350B VAL* 2.6 55.7 + - + +
351B ILE* 3.7 2.2 - - - +
352B GLU* 3.2 45.1 - - + +
359B ARG* 3.1 8.6 + - - -
360B LYS* 1.3 72.4 - - - +
362B GLY* 1.3 58.1 + - - +
370B PHE* 4.3 15.5 - - + -
372B PRO* 3.7 6.3 - - + +
373B ALA* 3.1 20.6 + - - +
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Residues in contact with GLY 362 (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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350B VAL 2.8 24.6 + - - +
360B LYS* 3.2 20.2 + - - -
361B ILE* 1.3 82.3 - - - +
363B TYR* 1.3 62.6 + - - -
370B PHE* 4.2 6.5 - - - -
371B VAL 3.4 12.3 - - - -
372B PRO 4.5 0.2 - - - -
373B ALA* 4.1 7.9 - - - -
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Residues in contact with TYR 363 (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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347B THR* 3.8 23.3 - - + -
348B LEU 3.2 9.6 - - - +
349B HIS* 4.5 1.6 - - + +
350B VAL* 4.3 1.6 - - - +
360B LYS* 4.0 15.5 - - - +
362B GLY* 1.3 76.0 - - - +
364B TRP* 1.3 65.4 + - - +
365B ASN* 4.0 23.8 - - - -
368B ASP* 4.3 7.8 + - + -
369B LYS 3.9 0.4 - - - +
370B PHE* 3.3 6.5 - - - -
371B VAL* 3.0 68.9 + - + +
372B PRO 5.9 0.4 - - - -
373B ALA* 6.6 0.4 - - - -
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Residues in contact with TRP 364 (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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110B GLU 5.3 0.9 - - - -
113B GLU* 3.6 35.7 - - + -
114B ALA* 3.7 27.6 - - + -
117B SER* 3.3 24.4 + - - -
118B ILE* 4.8 1.3 - - + -
346B TYR* 3.8 30.5 - + - -
347B THR* 3.3 5.4 - - - -
348B LEU* 2.5 55.4 + - + +
350B VAL* 4.5 11.4 - - + -
363B TYR* 1.3 77.5 - - - +
365B ASN* 1.3 76.9 + - - +
366B GLU* 3.9 18.6 - - + -
369B LYS* 3.3 37.7 - - + +
370B PHE* 3.5 14.1 - - + -
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Residues in contact with ASN 365 (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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346B TYR 3.5 17.0 - - - +
347B THR* 4.2 9.8 + - - +
363B TYR* 4.0 14.5 - - + -
364B TRP* 1.3 86.4 - - - +
366B GLU* 1.3 58.4 + - - +
367B ASP* 2.8 7.9 + - - +
368B ASP* 2.4 59.6 + - - +
369B LYS* 2.8 29.2 + - - +
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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