Contacts of the helix formed by residues 368 - 382 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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172A VAL* 5.1 5.5 + - - -
174A PRO* 3.0 30.9 - - - +
355A PHE* 5.9 0.2 - - - -
366A ALA* 3.9 10.2 - - - +
367A LEU* 1.3 86.6 - - - +
369A TYR* 1.3 61.8 + - - +
370A GLY 3.0 0.4 - - - -
371A LEU* 2.9 22.8 + - - +
372A ILE* 2.9 24.7 + - - +
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Residues in contact with TYR 369 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174A PRO* 4.1 21.6 + - + -
175A HIS 3.7 18.9 + - - -
176A ALA 5.1 0.3 + - - -
358A TRP* 3.3 45.8 - + + +
364A GLN* 2.8 45.3 - - + +
365A PRO 3.8 10.8 - - - -
366A ALA 3.0 13.0 + - - +
367A LEU* 2.8 2.4 - - - +
368A SER* 1.3 80.2 + - - +
370A GLY* 1.3 56.3 + - - +
372A ILE* 3.4 14.0 + - + +
373A ALA* 3.0 27.2 + - - +
701A TYR* 5.3 6.5 + + - -
706A LEU* 5.6 7.4 - - + -
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Residues in contact with GLY 370 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355A PHE* 3.4 27.4 - - - +
358A TRP* 3.5 24.0 - - - +
367A LEU 2.9 9.6 + - - -
369A TYR* 1.3 76.9 - - - +
371A LEU* 1.3 58.9 + - - +
373A ALA* 3.1 4.6 + - - +
374A ALA* 3.0 27.2 + - - +
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Residues in contact with LEU 371 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355A PHE* 3.5 18.6 - - + -
368A SER* 2.9 16.9 + - - +
370A GLY* 1.3 75.9 - - - +
372A ILE* 1.3 61.5 + - + +
374A ALA* 3.4 9.7 + - + -
375A VAL* 3.0 47.3 + - + +
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Residues in contact with ILE 372 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162A TYR* 4.2 19.2 - - + +
173A PHE* 4.1 28.0 - - + -
174A PRO* 4.5 12.1 - - + -
177A PHE* 5.5 8.1 - - + -
368A SER* 2.9 43.2 + - - +
369A TYR* 3.7 13.2 - - + +
371A LEU* 1.3 81.4 - - + +
373A ALA* 1.3 58.8 + - - +
375A VAL* 3.9 6.0 - - - +
376A SER* 3.0 30.4 + - - -
707A LEU* 6.5 1.6 - - + -
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Residues in contact with ALA 373 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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354A SER* 4.3 13.0 - - - -
358A TRP* 3.8 29.2 - - + +
369A TYR 3.0 13.9 + - - +
370A GLY 3.1 9.2 + - - +
372A ILE* 1.3 77.6 - - - +
374A ALA* 1.3 64.1 + - - +
376A SER* 3.3 5.3 + - - -
377A VAL* 3.0 26.9 + - - +
696A ALA 4.2 7.9 - - - +
697A ALA* 4.4 6.9 - - - +
707A LEU* 5.8 2.2 - - + -
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Residues in contact with ALA 374 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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351A ALA* 3.8 26.4 + - + +
352A VAL* 5.6 0.4 - - - -
355A PHE* 4.8 5.2 - - + -
370A GLY 3.0 12.4 + - - +
371A LEU* 3.4 17.7 + - + +
373A ALA* 1.3 77.1 - - - +
375A VAL* 1.3 62.3 + - + +
377A VAL* 2.9 27.6 - - - +
378A LEU* 3.0 16.5 + - + +
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Residues in contact with VAL 375 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158A VAL* 3.6 25.4 - - + +
162A TYR* 3.4 46.7 - - + -
187A TYR* 6.2 0.4 - - + -
371A LEU* 3.0 37.4 + - + +
372A ILE* 3.9 4.5 - - - +
374A ALA* 1.3 74.5 - - + +
376A SER* 1.3 59.5 + - - +
378A LEU* 3.4 4.8 + - + +
379A ILE* 3.0 29.6 + - + +
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Residues in contact with SER 376 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162A TYR* 6.3 1.6 - - - -
187A TYR* 4.5 5.1 + - - -
372A ILE* 3.0 23.6 + - - -
373A ALA* 3.7 3.6 - - - -
374A ALA 3.2 0.2 - - - -
375A VAL* 1.3 76.9 - - - +
377A VAL* 1.3 59.1 + - - +
379A ILE* 2.9 23.2 - - - +
380A ILE* 3.0 17.2 + - - +
696A ALA* 3.9 9.7 - - - +
707A LEU* 5.2 1.8 - - - -
708A LEU* 3.0 42.0 - - - +
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Residues in contact with VAL 377 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347A VAL* 3.8 13.5 - - + +
350A VAL* 3.9 19.7 - - + -
351A ALA* 3.4 29.8 - - + -
354A SER* 5.5 1.8 - - - +
373A ALA 3.0 15.0 + - - +
374A ALA 2.9 22.7 - - - +
376A SER* 1.3 76.7 - - - +
378A LEU* 1.3 59.3 + - - +
380A ILE* 3.1 19.4 - - - +
381A ALA* 3.2 12.3 + - - +
693A VAL* 3.5 34.1 - - + +
696A ALA* 4.2 3.5 - - + +
697A ALA* 4.9 3.8 - - - +
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Residues in contact with LEU 378 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154A MET* 3.8 34.3 - - + +
155A GLY* 4.0 10.0 - - - -
158A VAL* 4.0 27.4 - - + -
347A VAL* 3.9 28.3 - - + +
348A ILE* 4.4 11.4 - - + -
351A ALA* 4.4 9.2 - - + -
374A ALA* 3.0 22.4 + - + +
375A VAL* 3.7 5.8 - - + +
377A VAL* 1.3 76.1 - - - +
379A ILE* 1.3 64.5 + - - +
381A ALA* 3.4 16.0 + - - +
382A CYS 3.6 4.2 + - - -
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Residues in contact with ILE 379 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155A GLY* 3.9 10.8 - - - +
158A VAL* 4.6 1.7 - - + +
159A ALA* 3.4 36.6 - - + -
187A TYR* 4.4 32.5 - - + -
190A ALA* 4.0 22.4 - - + -
191A ALA 5.2 0.4 - - - +
194A ILE* 4.7 9.8 - - + +
375A VAL* 3.0 19.9 + - + +
376A SER* 2.9 28.3 - - - +
378A LEU* 1.3 75.9 - - - +
380A ILE* 1.3 62.3 + - + +
381A ALA 3.4 0.3 + - - -
382A CYS* 3.6 14.9 + - - +
708A LEU* 5.2 2.9 - - + -
713A ALA* 5.5 5.4 - - + +
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Residues in contact with ILE 380 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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376A SER 3.0 17.0 + - - +
377A VAL* 3.1 24.5 - - - +
379A ILE* 1.3 76.6 - - + +
381A ALA* 1.3 58.7 + - - +
382A CYS 3.4 0.2 - - - -
689A ASN* 2.9 42.8 + - - +
692A GLY* 4.0 14.4 - - - +
693A VAL* 3.8 20.4 - - + -
696A ALA* 3.8 8.1 - - + -
708A LEU* 5.0 4.9 - - + -
712A ILE* 3.7 27.4 - - + -
713A ALA* 3.9 21.3 - - + +
716A ALA* 4.4 15.0 - - + -
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Residues in contact with ALA 381 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151A LEU* 5.0 0.9 - - + -
154A MET* 5.0 6.5 - - + -
343A PHE* 3.6 29.8 - - + -
347A VAL* 3.5 22.4 - - + -
377A VAL 3.2 19.0 + - - +
378A LEU* 3.5 8.1 - - - +
379A ILE 3.2 0.4 - - - -
380A ILE* 1.3 81.3 - - - +
382A CYS* 1.3 57.2 + - - +
383A PRO* 3.0 17.0 - - - +
686A PHE* 5.3 0.2 - - - -
689A ASN* 3.8 9.7 - - - +
693A VAL* 4.6 5.2 - - + -
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Residues in contact with CYS 382 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151A LEU* 3.5 14.6 - - - +
152A ILE* 3.2 49.4 - - - -
154A MET* 5.7 0.4 - - + +
155A GLY* 3.8 18.6 - - - -
156A ILE 4.3 1.8 - - - -
194A ILE* 3.7 31.4 - - + +
378A LEU 3.6 1.8 + - - +
379A ILE 3.6 12.0 + - - +
380A ILE 3.4 0.8 - - - -
381A ALA* 1.3 77.1 - - - +
383A PRO* 1.3 63.4 - - - +
384A CYS 4.0 0.3 + - - -
689A ASN* 3.0 12.5 + - - -
717A 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