Contacts of the helix formed by residues 368 - 382 (chain B) in PDB entry 3RFU
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 SER 368 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172B VAL* 5.1 5.2 + - - -
174B PRO* 3.0 30.4 - - - +
366B ALA* 3.9 10.5 - - - +
367B LEU* 1.3 85.4 - - - +
369B TYR* 1.3 62.9 + - - +
370B GLY 3.0 0.4 - - - -
371B LEU* 2.9 23.4 + - - +
372B ILE* 3.0 24.6 + - - +
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Residues in contact with TYR 369 (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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174B PRO* 4.1 21.0 + - + +
175B HIS 3.7 18.8 + - - -
176B ALA 5.1 0.3 + - - -
358B TRP* 3.3 45.1 - + + +
362B GLY* 6.1 0.2 - - - -
364B GLN* 2.9 47.1 - - + +
365B PRO 3.8 10.5 - - - -
366B ALA 3.0 14.3 + - - +
367B LEU* 2.8 2.2 - - - +
368B SER* 1.3 80.5 + - - +
370B GLY* 1.3 56.2 + - - +
372B ILE* 3.4 13.2 + - + +
373B ALA* 3.0 26.9 + - - +
701B TYR* 5.3 6.3 + + - -
706B LEU* 5.6 6.7 - - + -
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Residues in contact with GLY 370 (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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355B PHE* 3.4 27.4 - - - +
358B TRP* 3.5 24.0 - - - +
367B LEU 2.9 9.6 + - - -
369B TYR* 1.3 76.8 - - - +
371B LEU* 1.3 58.7 + - - +
373B ALA* 3.1 4.9 + - - +
374B ALA* 3.0 27.2 + - - +
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Residues in contact with LEU 371 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355B PHE* 3.5 18.9 - - + -
368B SER* 2.9 17.5 + - - +
370B GLY* 1.3 74.4 - - - +
372B ILE* 1.3 59.9 + - + +
374B ALA* 3.4 9.8 + - + -
375B VAL* 3.0 48.5 + - + +
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Residues in contact with ILE 372 (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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162B TYR* 4.2 19.4 - - + +
173B PHE* 4.1 28.3 - - + -
174B PRO* 4.5 11.7 - - + -
177B PHE* 5.5 7.9 - - + -
368B SER* 3.0 43.6 + - - +
369B TYR* 3.7 13.0 - - + +
371B LEU* 1.3 79.5 - - + +
373B ALA* 1.3 57.7 + - - +
375B VAL* 3.9 6.8 - - + +
376B SER* 3.0 30.7 + - - -
707B LEU* 6.5 1.3 - - + -
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Residues in contact with ALA 373 (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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354B SER* 4.3 12.8 - - - -
358B TRP* 3.8 28.7 - - + +
369B TYR 3.0 14.6 + - - +
370B GLY 3.1 8.9 + - - +
372B ILE* 1.3 76.9 - - - +
374B ALA* 1.3 65.7 + - - +
376B SER* 3.3 4.3 + - - -
377B VAL* 3.0 26.6 + - - +
696B ALA 4.2 9.3 - - - +
697B ALA* 4.4 6.9 - - - +
707B LEU* 5.8 3.1 - - + -
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Residues in contact with ALA 374 (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 ALA* 3.8 27.3 + - + +
352B VAL* 5.6 0.4 - - - -
355B PHE* 4.8 4.9 - - + -
370B GLY 3.0 12.3 + - - +
371B LEU* 3.4 18.4 + - + +
373B ALA* 1.3 76.5 - - - +
375B VAL* 1.3 62.0 + - + +
377B VAL* 2.9 27.0 - - - +
378B LEU* 3.0 15.8 + - + +
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Residues in contact with VAL 375 (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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158B VAL* 3.6 25.9 - - + +
162B TYR* 3.4 46.9 - - + -
187B TYR* 6.2 0.2 - - + -
371B LEU* 3.0 36.4 + - + +
372B ILE* 3.9 4.9 - - - +
374B ALA* 1.3 75.8 - - + +
376B SER* 1.3 58.3 + - - +
378B LEU* 3.4 4.8 + - - +
379B ILE* 3.0 30.0 + - + +
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Residues in contact with SER 376 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162B TYR* 6.3 1.3 - - - -
187B TYR* 4.5 4.9 + - - -
372B ILE* 3.0 24.9 + - - -
373B ALA* 3.7 4.0 - - - -
375B VAL* 1.3 77.1 - - - +
377B VAL* 1.3 60.5 + - - +
379B ILE* 3.0 23.8 - - - +
380B ILE* 3.0 17.9 + - - +
696B ALA* 3.9 8.9 - - - +
707B LEU* 5.2 1.6 - - - -
708B LEU* 3.0 42.2 - - - +
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Residues in contact with VAL 377 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347B VAL* 3.8 11.8 - - + +
350B VAL* 3.9 20.0 - - + -
351B ALA* 3.4 29.6 - - + -
354B SER* 5.5 1.8 - - - +
373B ALA 3.0 15.7 + - - +
374B ALA 2.9 22.4 - - - +
376B SER* 1.3 77.4 - - - +
378B LEU* 1.3 59.2 + - - +
380B ILE* 3.1 20.5 - - - +
381B ALA* 3.2 12.0 + - - +
693B VAL* 3.5 33.7 - - + +
696B ALA* 4.2 4.2 - - + +
697B ALA* 4.9 3.8 - - - +
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Residues in contact with LEU 378 (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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154B MET* 3.9 33.2 - - + +
155B GLY* 4.0 9.5 - - - -
158B VAL* 4.0 28.3 - - + -
347B VAL* 3.9 28.5 - - + +
348B ILE* 4.4 11.7 - - + -
351B ALA* 4.4 9.2 - - + -
374B ALA* 3.0 22.9 + - + +
375B VAL* 3.7 5.4 - - - +
377B VAL* 1.3 76.5 - - - +
379B ILE* 1.3 64.5 + - - +
381B ALA* 3.4 15.4 + - - +
382B CYS 3.6 4.7 + - - -
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Residues in contact with ILE 379 (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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155B GLY* 3.9 11.4 - - - +
158B VAL* 4.6 1.7 - - + +
159B ALA* 3.4 35.9 - - + -
187B TYR* 4.4 34.8 - - + -
190B ALA* 4.0 21.3 - - + -
191B ALA 5.2 0.2 - - - +
194B ILE* 4.7 9.9 - - + +
375B VAL* 3.0 18.8 + - + +
376B SER* 3.0 28.7 - - - +
378B LEU* 1.3 76.3 - - - +
380B ILE* 1.3 61.2 + - + +
381B ALA 3.4 0.3 + - - -
382B CYS* 3.6 14.9 + - - +
708B LEU* 5.2 2.7 - - + -
713B ALA* 5.5 5.8 - - + +
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Residues in contact with ILE 380 (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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376B SER 3.0 17.6 + - - +
377B VAL* 3.1 24.0 - - - +
379B ILE* 1.3 76.9 - - + +
381B ALA* 1.3 59.5 + - - +
382B CYS 3.4 0.2 - - - -
689B ASN* 2.9 43.3 + - - +
692B GLY* 4.0 14.4 - - - +
693B VAL* 3.8 20.6 - - + +
696B ALA* 3.8 8.3 - - + -
708B LEU* 5.0 4.3 - - + -
712B ILE* 3.7 28.0 - - + -
713B ALA* 3.9 22.0 - - + +
716B ALA* 4.4 14.4 - - + -
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Residues in contact with ALA 381 (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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151B LEU* 5.0 0.9 - - + -
154B MET* 5.0 6.3 - - + -
343B PHE* 3.6 29.2 - - + -
347B VAL* 3.5 23.1 - - + -
377B VAL 3.2 19.2 + - - +
378B LEU* 3.5 7.6 - - - +
379B ILE 3.2 0.4 - - - -
380B ILE* 1.3 80.3 - - - +
382B CYS* 1.3 58.4 + - - +
383B PRO* 3.0 16.3 - - - +
686B PHE* 5.3 0.2 - - - -
689B ASN* 3.8 9.7 - - - +
693B VAL* 4.6 4.9 - - + -
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Residues in contact with CYS 382 (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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151B LEU* 3.4 14.1 - - - +
152B ILE* 3.2 49.4 - - - -
154B MET* 5.6 0.6 - - + +
155B GLY* 3.7 20.0 - - - -
156B ILE 4.3 1.3 - - - -
194B ILE* 3.7 30.2 - - + +
378B LEU 3.6 1.4 + - - -
379B ILE 3.6 11.7 + - - +
380B ILE 3.4 1.0 - - - -
381B ALA* 1.3 76.3 - - - +
383B PRO* 1.3 63.4 - - - +
384B CYS 4.0 0.5 + - - -
689B ASN* 3.0 11.6 + - - -
717B MET* 5.8 1.9 - - - +
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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