Contacts of the helix formed by residues 548 - 555 (chain A) in PDB entry 2IUK
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 HIS 548 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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175A TYR 3.5 2.2 - - - -
177A PRO* 3.8 6.5 - - + +
188A ARG* 3.5 11.3 - - - +
544A LEU* 3.8 15.1 - - + +
545A SER 2.7 30.6 + - - +
546A VAL 3.4 0.4 - - - -
547A LEU* 1.3 69.8 - - - +
549A PRO* 1.3 84.2 - - + +
550A ILE* 3.0 20.8 + - + +
551A TYR* 2.9 19.6 + - + +
552A LYS* 3.3 14.2 + - - +
659A TYR* 3.1 26.9 - - - -
668A ASP* 2.9 24.7 + - - -
670A GLU* 3.2 22.7 - - + +
671A LEU* 4.5 3.7 + - + -
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Residues in contact with PRO 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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174A THR* 3.7 18.4 - - + -
175A TYR 3.3 17.7 - - - +
176A LEU* 3.5 24.7 - - + +
547A LEU 3.8 1.5 - - - +
548A HIS* 1.3 95.0 - - + +
550A ILE* 1.3 64.2 + - + +
552A LYS* 3.6 0.6 + - + -
553A LEU 3.4 9.7 + - - -
654A TYR* 2.6 34.8 + - + +
658A TYR* 3.9 34.5 - - + -
659A TYR* 4.5 0.2 - - - +
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Residues in contact with ILE 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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540A THR* 4.9 0.2 - - - +
544A LEU* 3.8 14.5 - - + +
548A HIS* 3.0 12.5 + - + +
549A PRO* 1.3 75.1 - - - +
551A TYR* 1.3 61.0 + - - +
553A LEU* 3.7 25.8 - - + -
554A LEU* 3.6 25.0 - - + +
654A TYR* 4.4 7.0 - - + -
655A VAL* 4.0 11.9 - - + -
659A TYR* 3.5 31.4 - - + +
671A LEU* 3.8 19.7 - - + -
674A TRP* 4.6 2.2 - - + -
701A LEU* 4.0 22.0 - - + -
705A CYS* 4.0 18.4 - - - -
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Residues in contact with TYR 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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540A THR* 3.8 21.3 - - + -
541A ASN* 4.5 7.9 + - - -
544A LEU* 3.5 26.0 - - + +
545A SER 3.3 13.5 - - - +
546A VAL* 3.5 46.2 - - + +
548A HIS* 2.9 15.5 + - + +
550A ILE* 1.3 75.2 - - - +
552A LYS* 1.3 66.8 + - + +
553A LEU 3.2 0.2 - - - -
555A TYR* 2.9 85.9 + + + +
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Residues in contact with LYS 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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171A VAL 4.9 0.6 + - - -
172A ASN* 2.9 32.5 + - - +
173A ASP 3.6 9.1 + - - -
174A THR* 3.1 27.4 + - + +
546A VAL 3.2 25.1 - - - +
547A LEU* 4.6 2.2 - - - +
548A HIS 3.3 10.9 + - - +
549A PRO 3.7 0.9 - - - +
551A TYR* 1.3 83.5 - - + +
553A LEU* 1.3 55.3 + - - +
555A TYR* 5.2 1.6 - - - -
556A PRO* 3.6 6.9 - - - +
654A TYR* 3.6 15.9 - - - +
793A ARG* 2.7 28.5 + - - -
798A TRP* 3.1 31.5 + - + +
799A THR* 4.6 4.0 - - - -
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Residues in contact with LEU 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 PRO 3.4 13.0 + - - +
550A ILE* 3.7 28.9 - - + -
551A TYR 3.2 0.4 - - - -
552A LYS* 1.3 81.2 - - - +
554A LEU* 1.3 67.3 + - + +
556A PRO* 3.3 2.6 - - - +
557A HIS* 3.3 19.4 + - - +
650A TRP* 4.0 24.7 - - + +
651A VAL* 4.2 16.6 - - + -
654A TYR* 3.5 37.9 + - + -
655A VAL* 5.0 0.2 - - + -
705A CYS* 3.8 27.1 - - + -
709A VAL* 5.3 2.0 - - + -
793A ARG* 3.3 17.1 + - - +
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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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540A THR* 4.6 2.7 - - + +
550A ILE* 3.6 21.7 + - + +
551A TYR 3.4 1.8 + - - +
553A LEU* 1.3 93.4 - - + +
555A TYR* 1.3 66.0 + - - +
556A PRO* 3.3 2.9 - - - -
557A HIS* 2.9 26.5 + - + +
558A TYR* 3.4 34.0 + - + +
674A TRP* 3.7 28.3 - - + -
705A CYS* 4.0 15.5 - - + +
708A ILE* 4.0 15.7 - - + -
709A VAL* 3.7 27.4 - - + -
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Residues in contact with TYR 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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210A TYR* 3.8 3.3 + - - -
266A ASP* 5.6 5.7 + - + +
267A GLU* 3.5 21.1 + - - -
269A PHE* 5.2 13.9 - + - -
540A THR* 4.4 1.6 - - + -
541A ASN* 2.8 44.3 + - - -
551A TYR* 2.9 63.4 + + + +
552A LYS* 4.9 1.6 - - - +
554A LEU* 1.3 70.5 - - - +
556A PRO* 1.4 65.7 - - + +
558A TYR* 3.2 33.9 + + + +
559A ARG* 3.9 5.1 + - + +
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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