Contacts of the helix formed by residues 542 - 559 (chain B) in PDB entry 5UFL
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 PRO 542 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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505B GLN 5.0 9.2 - - - +
507B PRO* 4.9 11.4 - - + -
510B ILE* 4.0 15.8 - - + +
540B ASP 3.4 9.8 - - - +
541B PHE* 1.4 92.1 - - + +
543B ALA* 1.3 63.1 + - - +
544B LEU* 3.2 4.0 - - + +
545B VAL* 3.4 26.2 - - + +
546B LEU* 3.3 19.9 + - - +
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Residues in contact with ALA 543 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
526A GLN* 3.3 3.8 - - - +
529A LEU* 3.2 20.0 - - + +
530A ARG* 6.1 2.2 - - - -
533A LEU* 4.0 26.0 - - + -
541B PHE* 2.9 22.6 + - + +
542B PRO* 1.3 71.9 - - - +
544B LEU* 1.3 58.1 + - + +
546B LEU* 3.5 2.1 + - - -
547B GLY 3.0 22.3 + - - -
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Residues in contact with LEU 544 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
526A GLN* 2.6 46.3 + - + +
530A ARG* 5.5 9.9 - - - +
542B PRO* 3.2 2.4 - - + -
543B ALA* 1.3 77.3 - - + +
545B VAL* 1.3 62.9 + - - +
547B GLY 3.3 0.5 + - - -
548B GLU* 3.1 13.6 + - - +
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Residues in contact with VAL 545 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
464B THR* 6.0 4.2 - - + +
507B PRO* 5.6 3.4 - - + +
510B ILE* 3.8 18.8 - - + -
542B PRO* 3.4 36.3 + - + +
544B LEU* 1.3 75.3 - - - +
546B LEU* 1.3 64.3 + - - +
548B GLU* 3.4 18.3 + - + +
549B SER* 2.9 27.9 + - - -
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Residues in contact with LEU 546 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
529A LEU* 3.7 19.3 - - + -
510B ILE* 3.5 38.8 - - + +
513B LEU* 4.0 15.7 - - + -
514B ALA* 4.2 2.2 - - + +
517B LEU* 4.8 0.9 - - + -
532B LEU* 3.4 35.7 - - + -
541B PHE* 3.9 11.2 - - + -
542B PRO 3.3 9.0 + - - +
543B ALA* 3.6 8.7 - - - +
544B LEU 3.3 0.2 - - - -
545B VAL* 1.3 79.9 - - - +
547B GLY* 1.3 54.8 + - - +
549B SER* 3.7 0.3 - - - -
550B ILE* 2.8 60.5 + - + +
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Residues in contact with GLY 547 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
522A ARG* 4.7 0.6 - - - +
525A VAL* 3.2 26.2 - - - +
526A GLN* 3.5 23.8 - - - -
529A LEU* 3.6 6.6 - - - +
543B ALA 3.0 11.9 + - - -
544B LEU 3.3 0.4 + - - -
546B LEU* 1.3 75.7 - - - +
548B GLU* 1.3 61.4 + - - +
551B ALA* 3.1 23.0 + - - +
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Residues in contact with GLU 548 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
522A ARG* 3.7 38.6 + - - +
526A GLN* 3.9 6.7 + - - +
464B THR* 4.4 21.9 + - + +
544B LEU* 3.1 16.0 + - - +
545B VAL* 3.6 18.4 - - + +
547B GLY* 1.3 75.0 - - - +
549B SER* 1.3 58.4 + - - +
551B ALA* 3.5 1.6 + - - +
552B ALA* 3.0 31.6 + - - +
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Residues in contact with SER 549 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
464B THR* 4.9 9.4 - - - -
465B LYS 4.1 8.0 + - - -
510B ILE* 4.0 11.9 - - - -
511B THR* 4.1 13.4 + - - -
514B ALA* 3.2 19.7 - - - +
545B VAL* 2.9 19.7 + - - -
546B LEU 3.2 4.5 + - - -
548B GLU* 1.3 74.2 - - - +
550B ILE* 1.3 60.8 + - - +
552B ALA* 3.8 4.3 - - - +
553B ASN* 2.7 43.1 + - - +
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Residues in contact with ILE 550 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
517A LEU* 3.2 33.9 - - + +
525A VAL* 3.6 16.8 - - + -
529A LEU* 4.4 12.6 - - + -
514B ALA* 4.1 13.9 - - - -
517B LEU* 3.9 24.2 - - + -
518B THR* 3.4 13.8 - - + +
546B LEU* 2.8 52.6 + - + +
549B SER* 1.3 70.6 - - - +
551B ALA* 1.3 59.7 + - - +
553B ASN 3.3 0.9 + - - -
554B ASN* 2.8 39.4 + - - +
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Residues in contact with ALA 551 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
519A SER 3.7 10.8 - - - -
520A ASP 3.6 16.1 - - - +
522A ARG* 3.6 31.0 - - + -
525A VAL* 3.7 8.7 - - + +
547B GLY 3.1 18.8 + - - +
548B GLU 3.9 3.8 - - - +
550B ILE* 1.3 76.6 - - - +
552B ALA* 1.3 57.0 + - - +
554B ASN* 3.4 1.9 + - - +
555B ALA* 2.9 28.9 + - - +
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Residues in contact with ALA 552 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
464B THR* 3.4 23.6 - - + +
466B VAL* 4.0 15.9 - - + +
548B GLU 3.0 19.2 + - - +
549B SER* 3.8 4.3 - - - +
551B ALA* 1.3 77.1 - - - +
553B ASN* 1.3 57.1 + - - +
555B ALA* 3.3 8.2 + - - +
556B TYR* 3.1 27.9 + - - +
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Residues in contact with ASN 553 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
465B LYS 3.2 22.4 + - - -
466B VAL* 4.1 4.5 - - - +
467B ALA* 3.0 32.2 + - - +
514B ALA* 3.6 8.7 - - - +
515B PHE* 3.3 17.3 - - - -
518B THR* 3.6 23.1 + - + +
549B SER* 2.7 36.3 + - - +
550B ILE 3.8 2.7 - - - +
552B ALA* 1.3 73.0 - - - +
554B ASN* 1.3 61.6 + - - +
556B TYR* 4.0 2.2 - - - +
557B ARG* 3.1 35.6 + - - +
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Residues in contact with ASN 554 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
517A LEU 2.9 27.5 + - - -
518A THR 3.2 16.5 - - - +
519A SER 3.0 29.7 + - - +
520A ASP* 4.3 0.2 - - - -
554A ASN* 3.3 19.6 - - - +
558A GLN* 5.1 2.0 + - - +
518B THR* 3.2 16.4 - - - +
550B ILE* 2.8 26.8 + - - +
551B ALA 3.6 1.1 - - - +
553B ASN* 1.3 73.7 - - - +
555B ALA* 1.3 65.3 + - - +
557B ARG* 4.9 2.0 - - - -
558B GLN* 3.1 37.4 + - - +
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Residues in contact with ALA 555 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
520A ASP* 3.6 24.1 - - + +
551B ALA 2.9 14.2 + - - +
552B ALA* 3.3 11.6 + - - +
554B ASN* 1.3 78.1 - - - +
556B TYR* 1.3 62.0 + - - +
558B GLN* 4.0 3.7 - - - +
559B GLN* 3.3 20.6 + - - +
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Residues in contact with TYR 556 (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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466B VAL* 3.1 34.5 - - + -
467B ALA 3.3 23.7 + - - -
468B ASP* 3.5 30.1 + - + +
552B ALA 3.1 12.2 + - - +
553B ASN* 3.6 2.7 + - - +
555B ALA* 1.3 73.8 - - - +
557B ARG* 1.3 75.3 + - + +
559B GLN* 2.9 49.9 + - - +
560B GLU* 3.6 15.7 + - - +
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Residues in contact with ARG 557 (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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558A GLN* 3.5 32.7 + - + +
467B ALA* 3.4 30.8 + - + +
473B LYS* 4.3 18.0 - - - +
515B PHE* 3.2 28.0 + - - +
518B THR* 2.9 43.6 + - - -
519B SER* 4.5 10.5 + - - +
520B ASP* 5.5 0.8 + - - +
524B GLN* 5.3 2.6 + - - +
553B ASN* 3.1 18.2 + - - +
554B ASN 4.4 1.6 - - - +
556B TYR* 1.3 93.3 - - + +
558B GLN* 1.3 61.6 + - - +
560B GLU* 3.0 26.6 + - - +
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Residues in contact with GLN 558 (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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518A THR* 2.8 28.5 + - - -
520A ASP* 4.0 20.9 + - - +
554A ASN* 5.2 1.6 + - - +
557A ARG* 3.4 50.2 + - + +
558A GLN* 3.9 23.1 - - + +
560A GLU* 5.1 4.0 + - - -
554B ASN* 3.1 30.7 + - - +
555B ALA* 4.0 3.6 - - - +
557B ARG* 1.3 75.0 - - - +
559B GLN* 1.3 56.1 + - - +
560B GLU 3.4 3.0 + - - -
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Residues in contact with GLN 559 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
555B ALA 3.3 10.5 + - - +
556B TYR* 2.9 39.7 + - - +
558B GLN* 1.3 73.0 - - - +
560B GLU* 1.3 72.4 + - - +
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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