Contacts of the helix formed by residues 544 - 559 (chain A) in PDB entry 2WSK
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 544 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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518A HIS* 3.0 26.1 + - - +
519A GLY* 5.4 0.7 - - - -
542A GLN 3.7 1.1 + - - -
543A ALA* 1.3 71.1 - - - +
545A SER* 1.3 62.2 + - - +
546A GLY* 3.5 3.6 + - - -
547A LEU* 3.2 23.7 + - - +
548A THR* 2.7 27.0 + - - -
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Residues in contact with SER 545 (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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543A ALA 3.6 5.6 + - - -
544A SER* 1.3 70.7 + - - +
546A GLY* 1.3 66.6 + - - +
548A THR* 3.4 7.8 + - - -
549A ALA* 3.1 24.3 + - - +
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Residues in contact with GLY 546 (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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544A SER* 3.2 4.6 + - - -
545A SER* 1.3 80.3 - - - +
547A LEU* 1.3 55.9 + - - +
549A ALA* 3.3 5.1 + - - +
550A PHE* 2.9 27.5 + - - +
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Residues in contact with LEU 547 (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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493A ARG* 6.1 0.4 - - + -
496A ILE* 4.2 20.0 - - + -
497A HIS* 3.8 33.2 - - + +
500A LEU* 3.9 15.5 - - + -
516A ASP 3.7 11.7 - - - +
517A GLU 2.9 22.0 - - - +
518A HIS 4.1 0.2 - - - -
519A GLY* 3.7 24.5 - - - +
544A SER* 3.2 19.9 + - - +
546A GLY* 1.3 72.3 - - - +
548A THR* 1.3 54.4 + - - +
550A PHE* 3.2 7.8 + - + +
551A THR* 2.8 40.4 + - - +
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Residues in contact with THR 548 (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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187A TYR* 3.9 34.4 + - + +
191A LEU* 4.2 9.0 - - + +
517A GLU* 2.9 11.3 + - + -
518A HIS* 3.5 16.3 + - - +
543A ALA* 5.4 0.9 - - - +
544A SER 2.7 21.8 + - - -
545A SER* 3.6 8.8 - - - -
546A GLY 3.2 0.4 - - - -
547A LEU* 1.3 76.1 - - - +
549A ALA* 1.3 53.2 + - - +
551A THR* 3.1 4.3 + - - -
552A ALA* 2.8 34.5 + - + +
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Residues in contact with ALA 549 (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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545A SER 3.1 14.0 + - - +
546A GLY* 3.7 5.2 - - - +
548A THR* 1.3 80.2 - - - +
550A PHE* 1.3 57.4 + - - +
552A ALA* 3.8 6.8 - - - +
553A ALA* 2.9 31.9 + - - +
632A PRO* 5.2 0.2 - - - -
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Residues in contact with PHE 550 (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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497A HIS* 3.4 69.3 - + + +
500A LEU* 4.3 5.2 - - + -
501A THR* 4.1 0.2 - - - -
546A GLY 2.9 15.2 + - - +
547A LEU* 3.3 18.8 - - + +
549A ALA* 1.3 77.6 - - - +
551A THR* 1.3 66.1 + - - +
554A LEU* 3.4 31.4 + - + +
632A PRO* 3.4 48.6 - - + +
633A PHE* 3.9 26.2 - + - -
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Residues in contact with THR 551 (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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191A LEU* 4.2 5.2 - - + -
500A LEU* 3.8 16.9 - - + +
504A LEU* 4.3 13.5 - - + -
512A LEU* 3.9 31.6 - - + -
517A GLU* 3.5 26.1 + - + -
547A LEU 2.8 22.5 + - - -
548A THR 3.5 4.0 - - - -
550A PHE* 1.3 77.5 - - - +
552A ALA* 1.3 64.8 + - - +
554A LEU* 3.1 8.7 + - - +
555A ILE* 3.1 24.7 + - + +
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Residues in contact with ALA 552 (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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190A GLN 3.8 22.0 - - - +
191A LEU* 3.8 20.8 - - + +
548A THR* 2.8 20.8 + - + +
549A ALA* 3.3 8.5 + - - +
551A THR* 1.3 74.3 - - - +
553A ALA* 1.3 61.1 + - - +
555A ILE* 3.4 0.9 + - - +
556A HIS* 2.6 33.9 + - + +
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Residues in contact with ALA 553 (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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549A ALA 2.9 17.0 + - - +
552A ALA* 1.3 76.5 - - - +
554A LEU* 1.3 57.8 + - - +
556A HIS* 3.3 5.1 + - - +
557A LEU* 2.8 31.1 + - - +
631A PRO* 4.2 12.7 - - + +
632A PRO* 3.7 32.3 - - + -
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Residues in contact with LEU 554 (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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500A LEU* 3.8 9.0 - - + +
501A THR* 3.6 43.7 - - + +
504A LEU* 4.1 18.4 - - + -
505A LEU* 3.9 16.9 - - + +
550A PHE* 3.4 30.3 + - + +
551A THR* 3.1 10.3 + - - +
553A ALA* 1.3 79.9 - - - +
555A ILE* 1.3 62.3 + - - +
557A LEU* 3.2 9.3 + - + +
558A ARG* 3.0 22.9 + - - +
632A PRO* 3.7 24.7 - - + -
633A PHE* 4.2 9.4 - - + -
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Residues in contact with ILE 555 (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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152A ILE* 3.2 39.6 - - + +
191A LEU* 3.5 31.9 - - + +
192A GLY* 3.5 19.5 - - - +
193A ILE* 4.9 1.1 - - + -
504A LEU* 3.8 22.7 - - + -
512A LEU* 4.2 25.1 - - + -
551A THR* 3.1 15.4 + - + +
552A ALA 3.8 2.2 - - - +
554A LEU* 1.3 77.0 - - - +
556A HIS* 1.3 59.3 + - - +
558A ARG* 3.4 19.4 - - - +
559A LYS* 3.4 14.0 - - - +
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Residues in contact with HIS 556 (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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189A LYS 4.2 5.3 + - - -
190A GLN* 3.0 28.5 + - - -
191A LEU 3.5 17.4 + - - -
192A GLY* 3.8 10.1 - - - -
552A ALA* 2.6 27.6 + - + +
553A ALA* 4.0 5.6 - - - +
555A ILE* 1.3 74.2 - - - +
557A LEU* 1.3 67.3 + - - +
559A LYS* 3.6 29.3 + - + +
560A ARG* 3.6 18.2 - - - +
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Residues in contact with LEU 557 (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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505A LEU* 4.6 17.0 - - + -
553A ALA 2.8 17.3 + - - +
554A LEU* 3.2 11.9 + - + +
556A HIS* 1.3 75.7 - - - +
558A ARG* 1.3 56.2 + - - +
560A ARG* 2.7 63.5 + - - +
561A ILE* 3.5 17.1 + - + +
607A PHE* 4.0 15.0 - - + -
630A ILE* 3.7 30.1 - - + -
631A PRO 4.2 9.9 - - - +
654A VAL* 3.9 18.2 - - + -
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Residues in contact with ARG 558 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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149A GLY 4.3 8.4 + - - -
150A SER* 5.9 0.4 - - - +
151A THR 5.3 1.3 - - - -
152A ILE* 4.0 23.8 - - - -
504A LEU* 3.3 21.9 + - - +
505A LEU* 4.4 5.8 - - + +
506A SER 3.3 15.5 + - - -
508A GLY 2.7 30.1 + - - +
510A PRO* 3.1 28.8 - - - +
554A LEU 3.0 12.5 + - - +
555A ILE* 3.4 10.3 - - - +
557A LEU* 1.3 77.0 - - - +
559A LYS* 1.3 58.0 + - - +
561A ILE* 2.9 28.8 + - - +
564A LEU* 3.0 46.3 + - + +
565A VAL* 3.5 12.5 - - - +
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Residues in contact with LYS 559 (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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150A SER* 4.6 9.3 + - - +
152A ILE* 3.7 16.9 - - + +
192A GLY* 3.0 30.3 + - - -
194A THR* 4.2 13.7 - - - +
555A ILE* 3.4 20.0 - - - +
556A HIS* 3.8 28.5 - - + +
557A LEU 3.2 0.6 + - - -
558A ARG* 1.3 75.9 - - + +
560A ARG* 1.3 60.5 + - + +
561A ILE 3.4 0.4 - - - -
565A VAL* 3.7 22.0 - - - +
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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
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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