Contacts of the strand formed by residues 353 - 361 (chain B) in PDB entry 6RUT
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 THR 353 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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59B GLN* 4.3 10.5 - - - +
141B TYR* 3.4 17.0 - - - -
143B ILE* 3.7 29.8 - - + +
148B MET* 5.6 3.1 - - + -
170B PHE* 4.6 1.1 - - - -
172B LEU* 4.0 11.4 - - - +
343B PHE* 4.2 9.9 - - + -
344B TYR 3.4 11.4 - - - +
345B ASP* 3.6 3.6 + - - +
351B ASN* 4.5 7.4 - - - +
352B HIS* 1.3 97.6 + - - +
354B ALA* 1.3 68.7 + - - +
355B PHE* 5.5 8.3 - - + -
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Residues in contact with ALA 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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152B SER 4.3 4.7 - - - -
154B VAL* 3.4 32.1 - - + +
170B PHE* 4.1 10.3 - - + -
172B LEU* 3.9 16.8 - - + -
343B PHE* 3.5 3.4 - - - +
344B TYR* 2.7 41.0 + - + +
353B THR* 1.3 76.8 - - - +
355B PHE* 1.3 63.7 + - - +
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Residues in contact with PHE 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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143B ILE* 4.8 11.2 - - + -
145B LEU* 3.7 23.3 - - + -
148B MET* 4.0 22.2 - - + -
151B PRO* 3.8 22.9 - - + -
152B SER 3.3 26.3 + - - +
153B THR* 3.4 3.4 - - + +
154B VAL* 3.0 29.1 + - - +
177B PRO* 3.7 28.3 - - + -
180B TRP* 3.7 19.7 - + - -
203B VAL* 6.3 2.5 - - + -
341B VAL* 4.1 21.8 - - + -
342B SER 4.0 2.9 - - - +
343B PHE* 4.2 13.2 - + + -
344B TYR* 4.2 3.1 - - - -
353B THR* 5.5 6.3 - - + -
354B ALA* 1.3 77.3 - - - +
356B GLY* 1.3 59.9 + - - +
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Residues in contact with GLY 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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153B THR* 3.6 18.1 - - - +
156B ARG* 4.2 11.1 + - - -
177B PRO* 4.8 4.5 - - - +
178B THR* 5.9 1.2 + - - +
341B VAL* 5.5 0.2 - - - -
342B SER* 2.8 20.2 + - - -
343B PHE* 4.2 0.4 - - - +
344B TYR* 4.1 13.7 - - - -
355B PHE* 1.3 74.6 - - - +
357B LEU* 1.3 67.4 + - - +
358B VAL* 4.3 1.7 + - - +
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Residues in contact with LEU 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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156B ARG* 3.8 12.6 - - - +
340B VAL 3.5 2.6 - - - +
341B VAL* 3.2 4.2 - - - -
342B SER* 2.7 43.5 + - - +
356B GLY* 1.3 77.1 - - - +
358B VAL* 1.3 64.4 + - - +
359B ASP* 3.7 13.3 - - - +
491B TYR* 4.0 9.4 + - + -
495B PHE 3.2 27.4 - - - +
496B SER* 3.4 25.8 - - - +
497B LYS* 4.5 0.4 - - - -
498B SER* 3.3 26.2 - - - +
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Residues in contact with VAL 358 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177B PRO* 3.8 15.3 - - + -
178B THR* 3.2 58.3 + - + +
179B ASP* 5.5 0.2 - - - +
183B ILE* 4.3 12.1 - - + -
339B THR* 3.8 17.9 - - + -
340B VAL 3.6 3.6 - - - -
341B VAL* 3.7 16.6 - - + -
356B GLY 4.9 0.9 - - - +
357B LEU* 1.3 78.2 - - - +
359B ASP* 1.3 64.1 + - - +
360B HIS* 4.0 17.3 + - + -
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Residues in contact with ASP 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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339B THR* 3.4 1.8 - - - -
340B VAL* 2.7 44.8 + - + +
357B LEU* 3.7 11.0 - - - +
358B VAL* 1.3 75.1 - - - +
360B HIS* 1.3 63.1 + - - +
361B ILE* 3.7 2.0 + - - +
489B ILE* 4.0 15.0 - - + -
491B TYR* 3.6 13.8 + - - +
498B SER* 2.7 42.5 + - - +
500B VAL* 3.7 22.0 - - + +
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Residues in contact with HIS 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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179B ASP* 3.1 37.0 + - + +
182B GLU* 5.5 0.8 - - - +
183B ILE* 3.7 16.0 - - - +
186B LYS* 4.5 0.4 - - - -
334B LYS* 3.6 59.3 + - + +
337B GLY 6.1 0.2 - - - -
338B ALA 3.7 4.0 - - - +
339B THR* 3.0 30.3 + - + +
358B VAL* 4.0 13.1 + - + +
359B ASP* 1.3 70.9 - - - +
361B ILE* 1.3 61.8 + - - +
362B ASP* 3.0 12.0 + - - +
500B VAL* 3.9 16.2 - - - +
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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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204B LEU* 5.2 1.8 - - + -
330B ILE* 5.4 0.5 - - - +
334B LYS* 6.0 0.2 - - - -
337B GLY* 5.5 0.5 - - - -
338B ALA* 2.9 32.1 + - + +
339B THR 4.4 0.2 - - - +
340B VAL* 3.7 32.3 - - + -
359B ASP 4.2 4.0 - - - +
360B HIS* 1.3 67.9 - - - +
362B ASP* 1.3 62.9 + - - +
363B PRO* 3.6 1.9 - - - +
450B TYR* 2.6 30.7 + - - +
454B ILE* 3.7 24.7 - - + -
466B ILE* 3.8 17.9 - - + -
487B PHE* 3.7 33.4 - - + -
489B ILE* 3.9 14.6 - - + -
500B VAL* 4.4 7.9 - - + -
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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