Contacts of the strand formed by residues 356 - 360 (chain B) in PDB entry 5IXC
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 TYR 356 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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286B LEU* 4.2 2.4 - - - +
290B GLU* 2.6 29.5 + - - -
293B PHE* 5.2 0.2 - + - -
294B LEU* 3.5 28.8 - - + +
322B VAL* 3.7 32.3 - - + -
323B VAL 3.2 3.0 + - - -
324B GLY* 3.3 4.2 - - - -
325B ILE 2.7 30.4 + - - -
354B VAL* 3.3 9.4 - - - +
355B THR* 1.3 90.1 - - + +
357B PHE* 1.3 57.5 + - - +
458B PRO* 4.1 0.7 - - - -
459B LEU* 3.6 22.7 - - + -
461B LEU* 3.9 16.8 - - + -
659B MET* 3.8 17.9 - - + -
664B ARG* 3.4 31.3 - - + +
666B LEU* 4.1 12.6 - - + -
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Residues in contact with PHE 357 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325B ILE* 3.7 33.4 - - + -
327B ALA* 5.2 1.1 - - + -
338B LEU* 3.9 24.0 - - + -
342B LEU* 3.9 32.5 - - + -
356B TYR* 1.3 75.5 - - - +
358B SER* 1.3 63.8 + - - +
366B THR* 5.3 0.2 - - + -
367B MET* 3.3 34.6 - - + +
370B LEU* 5.0 1.1 - - + -
371B TYR* 3.9 26.0 - + - +
376B TRP* 4.2 13.2 - + - -
458B PRO* 4.0 14.1 - - + -
459B LEU 2.7 12.8 + - - +
460B PRO* 3.2 3.7 - - + +
461B LEU* 2.6 32.7 + - - +
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Residues in contact with SER 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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325B ILE 2.9 23.6 + - - +
326B MET* 3.6 2.8 - - - -
327B ALA* 3.1 21.7 + - - +
357B PHE* 1.3 80.2 - - - +
359B GLY* 1.3 60.0 + - - +
367B MET* 4.1 3.4 - - - -
461B LEU* 3.2 18.8 - - - -
655B SER* 2.5 34.2 + - - -
658B SER* 4.1 4.9 - - - -
659B MET* 3.6 18.9 - - - +
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Residues in contact with GLY 359 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327B ALA* 3.6 10.5 - - - -
358B SER* 1.3 76.1 - - - +
360B ILE* 1.3 64.1 + - - +
363B SER* 4.0 8.7 - - - -
364B THR* 3.8 9.1 - - - +
367B MET* 3.5 16.7 - - - -
461B LEU 3.1 6.6 + - - +
463B LEU* 3.1 26.5 + - - +
655B SER* 3.7 1.6 - - - -
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Residues in contact with ILE 360 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327B ALA 3.4 10.1 + - - +
328B THR 4.3 0.2 - - - -
329B GLY* 3.5 18.2 - - - +
359B GLY* 1.3 77.6 - - - +
361B SER* 1.3 83.9 + - - +
362B GLY 3.2 1.2 + - - -
363B SER* 3.0 17.1 + - - -
364B THR* 3.9 3.1 - - - -
463B LEU* 4.0 20.9 - - + +
480B TRP* 3.9 27.1 - - + -
527B TRP 5.1 1.6 - - - +
650B TYR 5.2 8.3 - - - +
653B ASN* 4.0 9.9 - - + +
654B THR* 3.4 31.2 - - - +
655B SER* 3.9 9.0 - - - +
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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