Contacts of the helix formed by residues 502 - 508 (chain A) in PDB entry 1XMI
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 ILE 502 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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501A THR* 1.3 70.5 - - - +
503A LYS* 1.3 65.3 + - - +
505A ASN* 3.3 8.0 + - - +
506A ILE* 3.1 40.7 + - + +
517A TYR* 4.9 0.4 - - - +
526A LEU* 5.6 5.2 - - + -
529A ASP* 4.4 20.0 - - + +
530A ILE* 5.4 7.2 - - + -
533A PHE* 4.5 10.3 - - + -
536A LYS 4.9 0.2 - - - +
537A ASP* 3.5 19.7 + - + +
539A ILE* 3.7 27.9 + - + -
541A LEU* 3.8 23.3 - - + -
548A LEU* 5.1 3.1 - - + -
556A ILE* 4.2 24.0 - - + -
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Residues in contact with LYS 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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501A THR* 3.3 3.8 - - - +
502A ILE* 1.3 79.5 - - - +
504A GLU* 1.3 57.4 + - + +
506A ILE* 3.2 1.6 + - - -
507A ILE* 2.9 46.5 + - + +
512A TYR* 3.7 35.8 + - + -
517A TYR* 3.5 26.1 + - + +
518A ARG* 5.3 3.3 - - - +
537A ASP* 3.3 38.0 + - - +
538A ASN* 5.2 10.9 + - - +
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Residues in contact with GLU 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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498A MET* 5.0 6.9 - - + +
499A PRO 4.7 1.7 - - - +
500A GLY* 3.6 12.3 - - - -
501A THR* 3.1 45.0 + - - +
503A LYS* 1.3 75.7 - - - +
505A ASN* 1.3 58.0 + - - +
507A ILE* 4.7 4.5 - - - -
508A ALA* 2.8 30.1 + - - +
532D LYS* 5.8 2.1 + - - -
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Residues in contact with ASN 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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497A ILE* 3.6 8.1 - - - +
498A MET* 2.7 57.8 + - - +
500A GLY* 3.7 9.1 + - - -
501A THR 2.9 24.4 + - - +
502A ILE* 3.6 8.3 - - - +
503A LYS 3.3 0.2 - - - -
504A GLU* 1.3 78.2 - - - +
506A ILE* 1.3 57.3 + - - +
508A ALA* 4.1 2.3 - - - +
541A LEU* 3.9 8.9 - - - +
556A ILE* 4.0 16.2 - - + -
560A ARG* 2.7 49.5 + - - +
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Residues in contact with ILE 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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502A ILE* 3.1 35.0 + - + +
503A LYS 3.2 3.3 + - - +
505A ASN* 1.3 77.6 - - - +
507A ILE* 1.3 65.3 + - - +
508A ALA* 4.3 0.2 - - - +
517A TYR* 3.9 25.4 - - + +
520A VAL* 4.5 4.5 - - + -
521A ILE* 3.9 24.2 - - + -
526A LEU* 4.2 12.6 - - + -
556A ILE* 4.3 10.5 - - + +
559A ALA* 3.9 23.8 - - + +
560A ARG* 3.5 23.2 - - - +
563A TYR* 3.8 26.5 - - + +
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Residues in contact with ILE 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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503A LYS* 2.9 33.5 + - + +
504A GLU* 4.3 3.4 - - - +
506A ILE* 1.3 77.3 - - - +
508A ALA* 1.3 66.1 + - - +
509A GLY 4.2 3.1 - - - +
510A VAL* 2.7 56.4 + - - +
512A TYR* 3.8 20.2 - - + +
517A TYR* 3.5 24.5 - - + -
563A TYR* 3.3 35.4 - - + +
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Residues in contact with ALA 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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498A MET* 4.7 7.9 - - - -
504A GLU 2.8 23.9 + - - +
505A ASN 4.1 11.9 - - - +
506A ILE 4.3 0.2 - - - +
507A ILE* 1.3 74.6 - - - +
509A GLY* 1.3 56.6 + - - +
510A VAL* 3.4 5.5 + - - +
560A ARG* 4.1 9.0 - - + +
670D SER* 3.2 38.8 - - - +
671D LEU* 4.2 20.9 - - + +
672D GLU 5.1 1.7 + - - +
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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