Contacts of the helix formed by residues 541 - 549 (chain W) in PDB entry 5IY8
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 541 (chain W).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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539W PHE* 3.4 3.4 - - - +
540W THR* 1.3 80.3 + - - +
542W TYR* 1.3 62.7 + - - +
543W GLN* 3.3 29.9 + - - +
544W TYR* 3.3 16.4 + - - +
545W MET* 3.4 19.2 + - - +
599W VAL* 3.3 16.3 - - - +
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Residues in contact with TYR 542 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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541W SER* 1.3 71.5 - - - +
543W GLN* 1.4 68.2 + - - +
545W MET* 3.2 9.0 + - - +
546W GLU* 2.7 46.6 + - - +
568W PHE 4.1 6.1 - - - -
569W ILE* 3.5 31.0 - - + -
570W GLU* 3.6 52.2 + - + +
572W GLN* 4.8 10.4 + - - -
599W VAL* 3.4 27.6 - - + +
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Residues in contact with GLN 543 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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541W SER* 3.3 15.2 + - - +
542W TYR* 1.4 96.7 + - - +
544W TYR* 1.3 54.2 + - - +
546W GLU* 3.4 15.2 + - - +
547W SER* 2.9 29.7 + - - -
555W GLN* 3.8 6.1 - - - +
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Residues in contact with TYR 544 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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509W GLU* 3.7 37.7 + - + +
510W THR* 5.2 9.9 - - + -
515W ALA* 6.0 0.2 - - - +
516W VAL* 3.7 20.4 - - + +
520W TYR* 3.1 54.6 - + - -
539W PHE* 3.5 22.0 - + + -
540W THR* 4.2 14.4 - - - -
541W SER* 3.3 24.5 + - - +
543W GLN* 1.3 73.4 - - - +
545W MET* 1.3 55.1 + - - +
547W SER* 3.2 4.8 + - - +
548W THR* 2.8 48.0 + - + -
621W PHE 4.5 2.2 - - - -
622W GLY* 5.8 1.8 - - - -
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Residues in contact with MET 545 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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539W PHE* 4.1 12.5 - - + -
541W SER 3.4 10.0 + - - +
542W TYR* 3.2 12.7 + - - +
544W TYR* 1.3 78.2 - - - +
546W GLU* 1.3 68.0 + - + +
548W THR* 3.1 18.4 + - - -
549W VAL* 3.3 12.5 + - - +
567W LEU* 4.5 7.9 - - + -
568W PHE 3.4 42.4 - - - +
569W ILE* 3.8 17.0 - - + +
597W LEU* 3.6 45.0 - - + +
598W SER* 4.1 13.0 - - - -
599W VAL* 4.3 10.1 - - - -
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Residues in contact with GLU 546 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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542W TYR* 2.7 32.9 + - - +
543W GLN* 3.7 10.3 + - - +
545W MET* 1.3 72.4 - - + +
547W SER* 1.4 67.3 + - - +
549W VAL 3.2 18.7 - - - +
550W ALA* 5.0 0.2 - - - -
553W TYR* 5.4 9.2 - - - +
555W GLN* 3.6 38.5 + - + +
559W GLU* 4.6 1.9 - - - +
569W ILE* 4.6 19.5 - - + -
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Residues in contact with SER 547 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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516W VAL* 3.6 20.7 - - - +
543W GLN 2.9 19.8 + - - -
544W TYR* 3.2 6.5 + - - -
546W GLU* 1.4 56.3 - - - +
548W THR* 1.3 64.3 + - - +
555W GLN* 3.4 23.1 + - - +
559W GLU* 2.6 42.0 + - - +
560W ASN 4.4 0.5 + - - -
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Residues in contact with THR 548 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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516W VAL* 3.8 28.3 - - + +
520W TYR* 4.7 10.1 - - + +
521W GLY* 4.7 7.0 - - - +
539W PHE* 3.1 40.2 - - + -
544W TYR* 2.8 36.4 + - + +
545W MET 3.1 10.4 + - - -
546W GLU 3.4 0.2 - - - -
547W SER* 1.3 75.4 - - - +
549W VAL* 1.3 56.8 + - - +
550W ALA 3.8 0.3 + - - -
560W ASN* 3.8 4.2 + - - +
561W ILE* 3.2 35.1 + - - +
597W LEU* 4.1 1.6 - - - +
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Residues in contact with VAL 549 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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524W LEU* 4.9 1.3 - - + -
545W MET 3.3 5.9 + - - +
546W GLU* 3.2 17.5 - - - +
548W THR* 1.3 73.8 - - - +
550W ALA* 1.4 64.6 + - - +
551W SER* 3.2 30.4 + - - +
553W TYR 4.6 2.4 - - - +
554W GLU* 5.4 0.2 - - - -
561W ILE* 3.5 31.4 - - + +
563W ARG 5.2 2.7 - - - +
565W LYS* 4.2 25.4 - - + -
597W LEU* 3.5 39.7 - - + -
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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