Contacts of the helix formed by residues 553 - 565 (chain A) in PDB entry 4IQJ
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 GLU 553 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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550A GLU 5.8 0.5 - - - +
551A LYS 4.2 0.4 + - - -
552A ASP* 1.3 79.6 + - - +
554A ARG* 1.3 65.4 + - - +
556A ARG* 2.6 63.9 + - - +
557A GLN* 4.8 5.1 + - - +
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Residues in contact with ARG 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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236A LEU* 5.8 5.7 - - - +
552A ASP* 3.4 19.3 + - - +
553A GLU* 1.3 79.1 - - + +
555A ILE* 1.3 60.1 + - + +
556A ARG 3.1 5.4 + - - -
557A GLN* 3.3 17.4 + - - +
558A VAL* 3.6 14.2 + - + +
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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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517A LYS* 5.9 4.0 - - + -
521A LEU* 4.2 29.4 - - + -
548A GLU* 3.3 28.3 - - + +
549A MET* 3.2 25.1 - - - +
552A ASP* 3.2 37.0 - - + +
554A ARG* 1.3 77.0 - - + +
556A ARG* 1.3 63.0 + - - +
557A GLN 3.4 0.7 - - - -
558A VAL* 3.9 16.1 - - + +
559A ILE* 3.4 28.9 + - + +
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Residues in contact with ARG 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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549A MET* 3.5 26.0 - - + +
552A ASP 4.6 4.7 - - - +
553A GLU* 2.6 60.7 + - - +
554A ARG 3.1 1.2 + - - -
555A ILE* 1.3 83.3 - - - +
557A GLN* 1.3 75.8 + - + +
560A GLU* 3.2 50.6 + - - +
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Residues in contact with GLN 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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222A ARG* 3.9 30.3 + - - +
553A GLU* 4.8 5.0 + - - +
554A ARG* 3.3 9.5 + - - +
556A ARG* 1.3 94.8 - - + +
558A VAL* 1.3 59.4 + - + +
560A GLU* 4.2 8.5 - - - +
561A VAL* 2.7 50.0 + - + +
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Residues in contact with VAL 558 (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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504A LEU* 4.0 31.6 - - + +
521A LEU* 5.6 7.9 - - + -
554A ARG* 3.6 17.9 - - + +
555A ILE* 4.0 17.7 - - + +
556A ARG 3.4 0.4 - - - -
557A GLN* 1.3 78.0 - - + +
559A ILE* 1.3 58.5 + - + +
561A VAL* 3.9 3.0 - - - +
562A ALA* 2.9 30.2 + - - +
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Residues in contact with ILE 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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504A LEU* 4.1 22.2 - - + -
521A LEU* 5.2 15.9 - - + -
535A LEU* 4.6 15.3 - - + -
538A ALA 6.5 0.7 - - - -
546A ARG* 6.3 2.5 - - + +
548A GLU* 5.9 2.9 - - + -
549A MET* 4.4 31.6 - - + +
555A ILE* 3.4 21.4 + - + +
556A ARG 4.2 2.0 - - - +
558A VAL* 1.3 75.4 - - + +
560A GLU* 1.3 57.0 + - - +
562A ALA* 3.0 2.8 + - - +
563A MET* 2.8 55.6 + - + +
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Residues in contact with GLU 560 (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 MET* 3.1 24.3 - - + +
556A ARG* 3.2 44.5 + - - +
557A GLN* 4.0 7.7 - - - +
559A ILE* 1.3 77.7 - - - +
561A VAL* 1.3 62.3 + - + +
563A MET* 3.2 29.5 - - + +
564A ARG* 3.3 13.5 + - - +
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Residues in contact with VAL 561 (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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222A ARG* 5.2 5.8 - - + -
223A ALA* 3.9 14.8 - - + +
226A VAL* 3.3 38.6 - - + -
557A GLN* 2.7 42.1 + - + +
558A VAL* 4.0 3.4 - - - +
560A GLU* 1.3 71.8 - - + +
562A ALA* 1.3 65.8 + - - +
564A ARG* 3.0 6.4 + - - -
565A LEU* 2.9 38.9 + - + +
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Residues in contact with ALA 562 (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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503A ALA* 3.9 29.8 - - + +
504A LEU* 3.9 15.9 - - + -
535A LEU* 3.7 15.9 - - + -
558A VAL 2.9 20.9 + - - +
559A ILE 3.0 4.4 + - - +
561A VAL* 1.3 77.8 - - - +
563A MET* 1.3 57.9 + - - +
565A LEU* 2.9 22.7 + - - -
566A GLU* 3.1 12.8 + - - +
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Residues in contact with MET 563 (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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24A LYS* 2.8 23.9 + - - -
535A LEU* 3.4 40.3 - - + +
536A GLN* 4.9 13.5 - - - +
546A ARG* 5.5 5.8 - - - +
549A MET* 5.9 2.2 - - + -
559A ILE* 2.8 42.3 + - + +
560A GLU* 3.2 26.9 - - + +
562A ALA* 1.3 72.9 - - - +
564A ARG* 1.3 58.1 + - - +
566A GLU* 3.6 10.9 - - - +
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Residues in contact with ARG 564 (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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22A ALA 4.5 6.9 - - - +
24A LYS* 3.3 18.6 - - - +
27A ASP* 3.7 23.5 + - - +
216A VAL* 3.9 15.4 - - - +
217A ARG* 4.0 27.9 - - - +
219A GLU* 6.0 1.0 - - - +
220A ASP* 2.7 42.5 + - + +
223A ALA* 3.8 21.1 - - + -
560A GLU 3.3 15.6 + - - +
561A VAL* 3.0 11.3 + - - +
563A MET* 1.3 79.0 - - - +
565A LEU* 1.3 61.8 + - + +
566A GLU 3.4 1.6 - - - -
568A LEU* 3.9 9.0 - - - +
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Residues in contact with LEU 565 (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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22A ALA* 6.1 1.3 - - + -
223A ALA* 3.4 35.2 - - + +
226A VAL* 3.7 22.0 - - + -
227A LEU* 4.3 11.9 - - + -
230A ILE* 4.0 24.9 - - + -
498A LEU 5.3 0.3 - - - +
499A ALA 4.9 0.2 - - - +
503A ALA* 4.7 5.5 - - - +
506A ASP* 4.3 11.0 - - - +
561A VAL* 2.9 30.3 + - + +
562A ALA* 2.9 10.2 + - - +
564A ARG* 1.3 83.2 - - - +
566A GLU* 1.3 63.3 + - - +
567A GLY 3.8 0.4 - - - -
568A LEU* 3.7 28.4 + - + +
570A ARG* 5.4 4.5 + - - -
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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