Contacts of the helix formed by residues 499 - 510 (chain A) in PDB entry 1IQ0
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 THR 499 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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497A GLN 3.9 9.0 - - - +
498A ALA* 1.3 79.6 - - - +
500A PRO* 1.3 76.8 - - - +
501A TYR* 2.9 26.9 + - + +
502A GLU* 2.5 36.3 + - - +
503A ARG* 3.2 11.6 + - - +
562A LEU* 5.2 4.0 - - + -
566A ARG* 4.0 14.6 + - - +
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Residues in contact with PRO 500 (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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499A THR* 1.3 88.0 - - - +
501A TYR* 1.3 60.8 + - + +
503A ARG* 3.8 12.0 - - + +
504A ALA* 3.0 30.8 + - - +
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Residues in contact with TYR 501 (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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499A THR* 2.9 18.9 + - - +
500A PRO* 1.3 79.3 - - + +
502A GLU* 1.3 66.5 + - - +
504A ALA* 4.1 3.5 - - - +
505A LEU* 3.2 17.3 + - - +
541A ALA 5.4 0.7 - - - -
542A TYR* 3.5 38.5 - + + -
545A ALA* 3.4 29.9 - - + +
546A ARG 4.7 0.5 + - - -
547A GLU* 2.5 37.2 + - - +
552A ALA* 3.8 23.1 - - + +
553A THR* 4.5 4.5 - - - +
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Residues in contact with GLU 502 (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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88A LEU* 4.4 6.3 - - + -
498A ALA* 4.0 13.9 - - + -
499A THR* 2.5 49.5 + - - +
501A TYR* 1.3 75.6 - - - +
503A ARG* 1.3 58.8 + - - +
505A LEU 3.4 0.5 + - - -
506A ALA* 2.9 32.9 + - - +
542A TYR* 2.6 33.6 + - - +
553A THR* 3.6 0.3 + - - -
562A LEU* 4.5 2.5 - - - +
565A LEU* 3.9 23.3 - - + -
566A ARG* 2.8 26.3 + - + -
569A LEU* 3.8 20.7 - - + +
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Residues in contact with ARG 503 (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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35A ASP* 2.7 40.4 + - - -
81A ARG* 4.6 7.9 - - - +
82A LEU 3.8 9.1 + - - +
84A THR* 2.8 52.7 + - + +
87A LEU* 3.1 30.6 - - + +
88A LEU* 4.5 6.2 - - + +
498A ALA* 5.3 1.3 - - + +
499A THR 3.2 9.5 + - - +
500A PRO* 3.8 12.8 - - + +
502A GLU* 1.3 79.5 - - - +
504A ALA* 1.3 63.8 + - - +
506A ALA* 3.3 5.6 + - - +
507A LEU* 3.0 26.4 + - + +
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Residues in contact with ALA 504 (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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27A ARG* 5.1 1.7 + - - +
500A PRO 3.0 19.3 + - - +
501A TYR* 4.1 4.5 - - - +
503A ARG* 1.3 78.3 - - - +
505A LEU* 1.3 62.1 + - - +
507A LEU* 3.4 10.3 + - - +
508A ASP* 3.3 26.6 + - - +
538A SER* 5.1 0.4 - - - -
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Residues in contact with LEU 505 (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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501A TYR 3.2 16.1 + - - +
502A GLU 3.9 2.2 - - - +
504A ALA* 1.3 75.8 - - - +
506A ALA* 1.3 66.7 + - - +
508A ASP* 3.1 10.6 + - - +
509A LEU* 3.2 14.3 + - + +
535A LEU* 4.5 4.3 - - + -
538A SER* 3.4 28.9 - - - +
539A TRP* 4.3 20.9 - - + +
542A TYR* 3.5 41.5 - - + -
569A LEU* 3.7 26.9 - - + +
573A LEU* 4.3 17.9 - - + -
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Residues in contact with ALA 506 (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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87A LEU* 3.5 22.9 - - + -
88A LEU* 3.8 14.1 - - + -
91A ALA* 3.6 20.5 - - + +
502A GLU 2.9 18.8 + - - +
503A ARG 3.6 0.7 - - - +
505A LEU* 1.3 76.2 - - - +
507A LEU* 1.3 62.9 + - - +
509A LEU* 3.0 16.5 + - - +
510A LEU* 3.1 14.4 + - - +
569A LEU* 4.1 12.3 - - + +
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Residues in contact with LEU 507 (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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27A ARG* 3.5 31.2 - - - +
35A ASP* 3.7 32.1 - - + +
36A TYR* 3.6 37.2 - - + +
82A LEU* 4.4 0.2 - - + -
87A LEU* 3.8 19.4 - - + +
503A ARG* 3.0 20.6 + - + +
504A ALA* 3.6 9.2 - - - +
505A LEU 3.2 0.2 - - - -
506A ALA* 1.3 77.4 - - - +
508A ASP* 1.3 62.4 + - - +
510A LEU* 3.0 25.1 + - + +
511A ASP* 3.7 9.0 - - - +
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Residues in contact with ASP 508 (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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27A ARG* 2.9 29.3 + - - +
504A ALA 3.3 12.0 + - - +
505A LEU 3.1 9.0 + - - +
507A LEU* 1.3 77.5 - - - +
509A LEU* 1.3 55.2 + - - +
511A ASP* 3.2 10.4 + - - +
531A TYR* 2.7 31.7 + - + -
534A ASP* 5.5 2.2 - - - -
535A LEU* 3.9 18.4 - - + -
538A SER* 2.6 31.0 + - - +
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Residues in contact with LEU 509 (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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91A ALA* 4.4 10.5 - - + +
505A LEU* 3.2 19.9 + - + +
506A ALA* 3.0 12.8 + - - +
508A ASP* 1.3 79.1 - - - +
510A LEU* 1.3 58.9 + - - +
511A ASP 3.1 1.7 + - - -
512A PHE* 3.4 18.4 + - - +
531A TYR* 3.5 2.2 - - - -
535A LEU* 4.0 18.2 - - + -
569A LEU* 3.6 34.3 - - + +
572A SER* 3.6 22.4 - - - +
573A LEU* 3.9 14.8 - - + +
576A THR* 3.6 34.0 + - + +
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Residues in contact with LEU 510 (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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1A MET* 5.5 4.9 - - - +
2A LEU* 4.1 27.1 - - + +
3A ARG* 3.9 14.9 + - - +
36A TYR* 3.4 20.2 - - - +
82A LEU* 4.2 8.3 - - + -
87A LEU* 3.9 28.3 - - + +
90A GLU* 3.3 28.5 - - + +
91A ALA* 3.5 27.6 - - + +
506A ALA 3.1 13.8 + - - +
507A LEU* 3.0 9.4 + - + +
509A LEU* 1.3 75.4 - - - +
511A ASP* 1.3 59.7 + - - +
512A PHE 3.4 1.0 + - - -
513A GLU* 4.7 5.5 + - - +
514A GLU* 5.1 1.6 + - - +
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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