Contacts of the strand formed by residues 339 - 347 (chain B) in PDB entry 3S95
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 LEU 339 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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334B PHE* 4.4 9.2 - - + -
335B ARG 4.1 7.4 - - - +
336B PRO 3.2 12.4 + - - +
337B SER 3.2 0.8 - - - -
338B ASP* 1.3 86.0 - - + +
340B ILE* 1.3 60.7 + - - +
341B HIS* 2.9 27.4 + - + -
356B VAL* 4.1 20.4 - - + -
357B THR 3.4 2.9 - - - -
358B HIS* 4.0 18.2 - - + +
359B ARG* 3.9 9.8 + - - -
365B MET* 3.9 26.7 - - + -
367B MET* 4.8 1.8 - - - -
403B LEU* 3.3 31.2 - - + -
412B ILE* 4.0 20.4 - - + -
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Residues in contact with ILE 340 (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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338B ASP 4.2 0.4 - - - -
339B LEU* 1.3 67.9 - - - +
341B HIS* 1.3 69.4 + - - +
342B GLY* 3.4 5.2 + - - +
356B VAL* 3.4 2.2 - - - -
357B THR* 2.8 52.2 + - + +
359B ARG* 3.3 52.3 - - + +
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Residues in contact with HIS 341 (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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336B PRO* 3.6 22.0 - - + -
339B LEU* 2.9 37.5 + - + +
340B ILE* 1.3 77.1 - - - +
342B GLY* 1.3 61.5 + - - +
354B ILE* 4.6 13.5 - - + -
355B LYS 4.0 3.8 - - - -
356B VAL* 4.3 6.3 - - + +
367B MET* 3.7 33.2 - - + +
405B LYS* 3.7 24.4 - - - +
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Residues in contact with GLY 342 (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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340B ILE* 3.4 5.5 + - - -
341B HIS* 1.3 75.4 - - - +
343B GLU* 1.3 67.2 + - - -
344B VAL* 3.6 3.3 + - - +
354B ILE* 3.6 9.7 - - - +
355B LYS* 2.7 22.4 + - - -
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Residues in contact with GLU 343 (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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342B GLY* 1.3 71.8 - - - -
344B VAL* 1.3 65.3 - - - +
345B LEU* 3.5 20.7 + - + +
354B ILE* 3.6 0.6 - - - -
355B LYS* 2.8 63.1 + - + +
415B TYR* 4.6 4.9 + - - -
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Residues in contact with VAL 344 (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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342B GLY 3.6 4.0 + - - +
343B GLU* 1.3 77.3 - - - +
345B LEU* 1.3 62.5 + - - +
346B GLY 3.9 23.6 - - - +
347B LYS* 4.4 7.2 - - + -
352B GLN* 3.9 25.1 - - + +
353B ALA 3.6 6.1 - - - +
354B ILE* 4.3 14.1 - - + +
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Residues in contact with LEU 345 (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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1B STU 3.5 64.2 - - + +
343B GLU* 3.8 37.7 - - + +
344B VAL* 1.3 73.7 - - - +
346B GLY* 1.3 55.6 + - - +
353B ALA 2.7 14.3 + - - +
354B ILE 4.4 0.2 - - - -
355B LYS* 3.9 17.9 - - + +
366B VAL* 3.6 34.1 - - + -
415B TYR* 4.1 13.7 - - + +
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Residues in contact with GLY 346 (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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1B STU 3.4 26.3 + - - -
344B VAL* 3.5 4.3 - - - +
345B LEU* 1.3 80.9 - - - +
347B LYS* 1.3 61.7 + - - -
352B GLN* 3.4 4.2 - - - +
353B ALA 2.9 27.7 + - - +
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Residues in contact with LYS 347 (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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1B STU 4.7 1.6 - - - +
344B VAL* 4.4 10.8 - - + -
346B GLY* 1.3 73.4 - - - +
348B GLY* 1.3 63.0 + - - +
351B GLY 4.0 0.2 - - - -
352B GLN* 4.0 18.2 - - + +
371B ILE* 4.5 8.1 - - + -
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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
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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