Contacts of the helix formed by residues 537 - 551 (chain A) in PDB entry 1Y8B
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 537 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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117A LEU* 3.2 5.8 - - - -
535A VAL* 3.4 7.3 - - - +
536A PRO* 1.3 78.0 - - - +
538A PRO* 1.3 79.2 - - - +
539A THR* 3.2 9.4 + - - -
540A ALA* 3.2 15.0 + - - +
541A ALA 3.5 5.2 + - - -
629A MET* 2.7 39.7 - - - +
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Residues in contact with PRO 538 (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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117A LEU* 3.3 12.5 - - + -
129A ASN* 4.3 10.3 - - - +
130A ALA* 4.1 15.0 - - + +
133A ALA* 3.1 36.8 - - + +
141A ALA* 6.4 0.2 - - + -
263A ALA* 4.1 11.9 - - + -
264A ALA* 6.1 1.6 - - + -
536A PRO 4.7 0.2 - - - +
537A SER* 1.3 88.6 - - - +
539A THR* 1.3 54.6 + - - +
541A ALA* 2.5 33.3 + - + +
542A THR* 2.7 16.3 + - + +
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Residues in contact with THR 539 (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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140A ASP 4.9 0.3 + - - -
141A ALA* 2.6 41.5 + - - +
144A GLY* 4.8 2.8 + - - -
145A SER* 3.0 25.6 + - - +
537A SER* 3.2 6.6 - - - -
538A PRO* 1.3 77.3 - - - +
540A ALA* 1.3 56.5 + - - +
541A ALA 2.5 13.2 + - - -
542A THR* 2.7 27.5 + - - +
543A LEU* 2.9 29.3 + - + +
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Residues in contact with ALA 540 (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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515A MET* 5.8 8.5 - - + -
518A MET* 6.3 2.0 - - - -
522A LYS* 3.9 13.7 + - - +
535A VAL* 3.7 25.6 - - + +
536A PRO* 4.4 11.0 - - + -
537A SER* 3.2 14.7 + - - +
539A THR* 1.3 80.9 - - - +
541A ALA* 1.3 58.8 + - - +
543A LEU* 4.3 8.7 - - - -
544A HIS* 3.4 20.4 + - - +
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Residues in contact with ALA 541 (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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115A PRO* 3.0 46.1 - - + +
116A GLN 4.9 2.0 - - - +
117A LEU* 5.6 1.3 - - + -
263A ALA 4.0 13.0 - - - +
264A ALA* 5.6 0.7 - - - -
535A VAL* 3.5 20.8 - - + +
537A SER 3.5 0.6 + - - -
538A PRO* 2.5 21.4 + - + +
539A THR 2.5 4.6 + - - -
540A ALA* 1.3 73.0 - - - +
542A THR* 1.3 64.2 + - - +
544A HIS* 3.2 2.8 + - - +
545A ALA 3.2 7.4 + - - -
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Residues in contact with THR 542 (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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115A PRO* 5.2 0.2 - - - -
138A LEU* 3.9 28.3 - - + -
141A ALA* 3.8 15.0 - - + +
261A VAL* 4.3 9.0 - - + -
263A ALA* 3.5 31.0 - - + +
538A PRO* 2.7 12.6 + - + +
539A THR* 2.7 31.1 + - - -
541A ALA* 1.3 71.3 - - - +
543A LEU* 1.3 70.8 + - - +
545A ALA* 2.9 22.3 + - - +
546A LEU* 3.2 12.4 + - - +
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Residues in contact with LEU 543 (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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138A LEU* 6.1 0.4 - - + -
142A LEU* 3.7 34.1 - - + -
145A SER* 4.6 2.7 - - - -
147A ILE* 3.5 38.6 - - + -
516A ALA* 5.8 3.4 - - - -
522A LYS* 5.4 2.5 - - - +
539A THR* 2.9 30.4 + - + +
540A ALA* 4.5 6.3 - - - +
542A THR* 1.3 82.1 + - - +
544A HIS* 1.3 56.9 + - - +
546A LEU* 2.7 34.4 + - + +
547A HIS* 3.1 31.0 + - + +
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Residues in contact with HIS 544 (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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115A PRO* 4.4 13.9 - - + -
522A LYS* 3.3 55.6 + - + +
523A GLY* 5.3 1.0 - - - -
525A GLN* 4.8 5.3 - - + +
526A LEU* 3.6 19.1 - - + +
530A ALA* 5.2 4.8 + - - +
531A ASN 5.0 10.0 + - - -
532A THR* 4.8 3.9 - - - -
533A ALA* 4.1 32.0 + - + +
535A VAL* 5.5 2.9 - - + -
540A ALA 3.4 18.3 + - - +
541A ALA* 3.2 8.4 + - - +
543A LEU* 1.3 78.5 - - - +
545A ALA* 1.3 57.0 + - - +
547A HIS* 4.3 6.0 - - - +
548A TYR* 3.0 29.3 + + + +
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Residues in contact with ALA 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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115A PRO* 4.1 17.9 - - + +
236A LEU* 4.6 13.9 - - + -
261A VAL* 6.2 2.7 - - + -
541A ALA 3.2 9.7 + - - +
542A THR* 2.9 15.8 + - - +
543A LEU 2.8 0.8 - - - -
544A HIS* 1.3 78.0 - - - +
546A LEU* 1.3 66.8 + - + +
548A TYR* 3.4 8.0 - - - +
549A HIS* 3.0 32.3 + - + -
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Residues in contact with LEU 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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138A LEU* 4.3 28.5 - - + -
142A LEU* 4.4 4.9 - - + -
170A VAL* 5.6 1.3 - - + -
173A PHE* 3.6 56.5 - - + -
174A LEU* 5.2 8.1 - - + -
176A GLU* 5.6 0.5 - - - +
177A SER* 6.3 1.3 - - - -
261A VAL* 6.5 1.1 - - + -
542A THR 3.4 13.9 - - - +
543A LEU* 2.7 34.7 + - + +
545A ALA* 1.3 72.7 - - + +
547A HIS* 1.3 59.4 + - + +
548A TYR 2.8 3.8 - - - -
549A HIS* 2.7 34.9 + - + +
550A GLN 3.4 6.1 + - - -
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Residues in contact with HIS 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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147A ILE* 4.7 12.5 - - + +
173A PHE* 3.5 34.7 - + - -
519A TYR* 3.6 43.8 - + + +
522A LYS* 5.1 4.0 - - - -
523A GLY* 4.5 17.3 - - - -
526A LEU* 4.2 2.2 - - + +
543A LEU* 3.5 35.4 + - + +
544A HIS* 4.6 7.0 - - - +
546A LEU* 1.3 77.6 - - + +
548A TYR* 1.3 60.8 + - - +
550A GLN* 3.4 14.3 + - - +
551A THR* 3.2 21.7 - - - +
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Residues in contact with TYR 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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234A ASN* 2.9 47.7 + - + -
236A LEU* 5.8 4.7 - - + -
526A LEU* 3.9 22.2 - - + +
530A ALA 4.3 8.5 - - - -
531A ASN* 3.5 27.2 + - - -
544A HIS* 3.0 27.3 + + + +
545A ALA* 3.4 11.4 - - - +
546A LEU 2.8 1.0 + - - -
547A HIS* 1.3 79.3 - - - +
549A HIS* 1.3 71.7 + + - +
551A THR 3.1 22.0 - - - +
552A ASN* 4.7 1.8 + - - -
553A VAL* 3.1 47.6 - - + +
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Residues in contact with HIS 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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173A PHE 4.9 2.2 - - - +
176A GLU* 3.6 15.0 - - + +
177A SER* 3.4 49.5 + - - +
233A ASN* 3.6 24.7 + - + -
234A ASN* 3.9 17.0 - - + +
236A LEU* 4.7 14.5 - - + +
545A ALA* 3.0 25.9 + - + +
546A LEU* 2.7 22.4 + - + +
548A TYR* 1.3 82.0 - + - +
550A GLN* 1.3 62.3 + - - +
551A THR 3.4 0.2 - - - -
552A ASN* 3.4 17.6 + - - +
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Residues in contact with GLN 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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173A PHE* 5.6 7.2 - - + -
176A GLU* 4.0 23.9 - - + +
546A LEU 3.4 3.7 + - - +
547A HIS* 3.6 16.2 - - - +
548A TYR 3.2 0.4 - - - -
549A HIS* 1.3 81.7 - - - +
551A THR* 1.3 77.6 + - - +
552A ASN* 3.7 4.3 + - - -
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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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523A GLY* 4.3 6.5 - - - +
526A LEU* 3.2 27.5 - - + +
527A ARG* 4.3 26.9 + - + +
547A HIS 3.2 19.5 + - - +
548A TYR 3.1 14.1 - - - +
550A GLN* 1.3 88.6 - - - +
552A ASN* 1.3 67.8 + - - +
553A VAL* 3.0 10.4 + - - +
556A VAL* 6.0 1.2 - - - +
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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