Contacts of the helix formed by residues 546 - 554 (chain A) in PDB entry 1YI1
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 GLN 546 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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142A ARG* 3.4 28.5 - - + +
143A HIS* 3.8 14.9 + - + +
146A GLY* 4.9 0.6 - - - -
543A MET 3.4 7.6 - - - +
544A ASN* 3.1 35.0 + - - +
545A VAL* 1.3 85.1 + - + +
547A GLU* 1.3 96.4 + - - +
548A LEU 3.0 6.0 + - - -
549A ALA* 3.2 21.5 + - - +
608A CYS* 5.3 0.4 - - - -
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Residues in contact with GLU 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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141A PRO* 3.4 9.0 - - - +
142A ARG 3.1 23.9 + - - -
143A HIS* 3.2 10.0 + - - +
146A GLY* 4.0 11.6 - - - -
517A LEU* 4.2 10.3 - - + -
518A PRO* 3.9 20.6 - - + -
521A ILE* 3.8 15.2 - - + +
544A ASN 3.5 10.8 - - - +
545A VAL 3.0 1.2 + - - -
546A GLN* 1.3 103.9 + - - +
548A LEU* 1.3 62.9 + - - +
549A ALA 3.1 2.0 - - - -
550A THR* 2.9 30.2 + - - +
551A ILE* 3.1 24.4 + - - +
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Residues in contact with LEU 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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517A LEU* 3.5 28.2 - - + +
541A PHE* 3.9 17.9 - - + -
545A VAL* 3.0 36.8 + - + +
546A GLN 3.0 1.0 - - - -
547A GLU* 1.3 74.8 - - - +
549A ALA* 1.3 65.8 + - - +
551A ILE* 3.4 6.2 + - + -
552A ARG* 3.1 19.6 + - - +
560A VAL* 5.0 5.8 - - + -
601A MET 5.6 0.2 - - - +
604A PHE* 4.0 26.9 - - + +
605A ALA* 4.2 7.6 - - + +
608A CYS* 3.7 16.9 - - + +
610A ILE* 3.3 26.6 - - + +
636A LEU* 6.0 2.5 - - + -
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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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142A ARG* 3.7 24.9 - - + +
546A GLN 3.2 14.0 + - - +
548A LEU* 1.3 80.2 - - - +
550A THR* 1.3 55.6 + - - +
552A ARG* 3.4 2.5 + - - +
553A VAL* 3.0 36.9 + - + +
608A CYS* 3.5 19.5 - - - -
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Residues in contact with THR 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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139A VAL* 4.0 22.7 - - + -
140A LEU 3.6 12.6 + - - +
141A PRO* 3.5 7.6 - - + +
142A ARG* 3.5 24.9 - - - +
521A ILE* 3.7 19.3 - - + -
547A GLU* 2.9 32.2 + - - +
549A ALA* 1.3 76.1 - - - +
551A ILE* 1.3 58.2 + - - +
552A ARG 3.2 0.2 + - - -
553A VAL* 4.8 0.4 - - - -
554A GLU* 2.8 42.0 + - + +
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Residues in contact with ILE 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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517A LEU* 3.4 37.5 - - + -
521A ILE* 3.6 20.2 - - + -
547A GLU 3.1 10.4 + - - +
548A LEU* 3.4 15.9 + - + +
550A THR* 1.3 75.4 - - - +
552A ARG* 1.3 62.2 + - - +
554A GLU 3.8 0.2 - - - -
555A ASN* 3.1 2.6 + - - -
556A LEU* 3.1 54.8 + - + +
558A VAL* 4.0 25.6 - - + +
560A VAL* 5.1 1.8 - - + -
610A ILE* 4.3 4.7 - - + -
634A PRO* 3.8 18.5 - - + +
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Residues in contact with ARG 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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548A LEU 3.1 14.3 + - - +
549A ALA 3.8 3.4 - - - +
551A ILE* 1.3 76.0 - - - +
553A VAL* 1.3 65.2 + - + +
555A ASN* 2.6 62.0 + - - +
608A CYS* 3.2 25.6 - - + +
609A GLY* 3.3 25.9 + - - +
610A ILE* 4.1 5.1 - - + +
611A PRO* 4.2 10.9 - - - +
634A PRO* 3.6 37.1 - - - +
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Residues in contact with VAL 553 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142A ARG* 3.9 25.1 - - - +
549A ALA* 3.0 21.7 + - + +
550A THR* 4.0 3.1 - - - +
552A ARG* 1.3 82.8 - - + +
554A GLU* 1.3 72.5 + - - +
555A ASN* 3.4 9.3 + - - +
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Residues in contact with GLU 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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137A ARG* 2.5 39.6 + - - +
138A ASN 4.3 4.0 - - - +
139A VAL* 3.7 30.8 - - + +
140A LEU* 4.0 17.3 + - - +
142A ARG* 5.5 1.1 + - - +
550A THR* 2.8 30.2 + - + +
553A VAL* 1.3 83.2 - - + +
555A ASN* 1.3 71.1 + - - +
556A LEU* 3.3 28.2 + - + +
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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