Contacts of the strand formed by residues 351 - 358 (chain B) in PDB entry 4EMS
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 ASP 351 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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344B PHE* 6.5 0.2 - - - -
349B PHE* 3.8 1.2 - - - +
350B LYS* 1.3 83.3 - - + +
352B TYR* 1.3 80.1 + - - +
366B VAL* 3.5 4.7 - - - +
367B TYR* 2.8 51.5 + - + +
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Residues in contact with TYR 352 (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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337B GLU* 2.7 39.5 + - + +
340B TRP* 6.4 0.9 - - + -
341B ALA* 3.8 28.7 - - + +
344B PHE* 3.9 20.6 - + + -
351B ASP* 1.3 89.4 + - - +
353B LYS* 1.3 64.4 + - - +
354B ILE* 4.0 17.9 - - + -
364B ILE* 4.1 20.0 - - + -
365B GLU 3.0 14.6 - - - +
366B VAL* 4.2 7.4 - - + -
367B TYR* 4.0 5.2 - - - -
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Residues in contact with LYS 353 (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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196B ASP* 5.9 5.5 + - - +
352B TYR* 1.3 77.7 - - - +
354B ILE* 1.3 72.0 + - - +
355B THR* 4.1 14.4 + - - +
363B LEU 3.6 1.4 - - - +
364B ILE* 3.4 2.1 - - - -
365B GLU* 2.9 49.8 + - - +
367B TYR* 3.9 20.0 - - + +
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Residues in contact with ILE 354 (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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304B VAL* 4.4 13.0 - - + -
307B HIS* 3.5 35.2 + - + +
337B GLU* 3.7 37.7 - - + +
352B TYR* 4.0 17.5 - - + -
353B LYS* 1.3 82.9 - - - +
355B THR* 1.3 65.0 + - - +
356B PRO* 4.2 3.8 - - - +
362B VAL* 3.8 28.9 - - + -
363B LEU 3.3 2.5 - - - -
364B ILE* 4.2 13.7 - - + -
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Residues in contact with THR 355 (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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193B LYS 3.9 12.6 - - - +
194B CYS* 3.6 28.4 - - + +
353B LYS* 4.1 17.2 + - - -
354B ILE* 1.3 76.7 + - - +
356B PRO* 1.3 76.4 - - + +
357B VAL* 3.9 0.7 - - - +
362B VAL* 4.2 2.0 - - - -
363B LEU* 2.8 43.8 + - - +
365B GLU* 4.4 9.5 + - - -
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Residues in contact with PRO 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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193B LYS* 3.8 15.1 - - + +
307B HIS* 3.9 20.9 - - + -
309B SER* 3.8 23.1 - - - -
354B ILE 4.2 5.2 - - - +
355B THR* 1.3 99.9 - - + +
357B VAL* 1.3 60.7 + - - +
358B GLY 5.4 0.2 - - - +
362B VAL* 3.8 12.1 - - + -
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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
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7A VAL* 4.3 7.6 - - - +
10A LEU* 4.0 2.5 - - + +
11A ASP* 5.1 0.5 - - - +
186B PHE* 3.8 23.1 - - + -
189B ALA* 3.7 28.6 - - + +
190B LEU* 3.8 23.8 - - + +
193B LYS* 3.6 24.9 - - + +
194B CYS* 3.6 26.9 - - - -
355B THR 3.6 5.4 + - - +
356B PRO* 1.3 78.1 - - - +
358B GLY* 1.3 61.5 + - - +
361B ARG 3.2 10.3 + - - +
362B VAL 4.1 2.5 - - - -
363B LEU 3.9 11.4 - - - +
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Residues in contact with GLY 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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7A VAL* 5.7 0.2 - - - -
10A LEU* 3.5 16.3 - - - +
11A ASP* 3.2 15.3 - - - -
186B PHE* 4.0 2.9 - - - -
357B VAL* 1.3 78.9 - - - +
359B GLY* 1.3 65.8 + - - +
360B LEU 3.2 3.4 - - - -
361B ARG* 3.0 21.0 + - - +
402B GOL 3.7 11.2 + - - -
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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