Contacts of the helix formed by residues 501 - 508 (chain B) 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 THR 501 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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500B GLY* 1.3 74.7 - - - -
502B ILE* 1.3 59.8 + - - +
503B LYS* 3.6 9.9 + - - +
504B GLU* 3.0 39.5 + - - +
505B ASN* 3.0 31.9 + - - -
539B ILE 3.6 29.6 - - - +
540B VAL* 5.4 0.4 - - - -
541B LEU* 4.1 0.9 - - - -
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Residues in contact with ILE 502 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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501B THR* 1.3 73.0 - - - +
503B LYS* 1.3 60.6 + - - +
505B ASN* 3.3 4.0 + - - +
506B ILE* 3.0 41.9 + - + +
526B LEU* 6.2 0.7 - - + -
529B ASP* 4.7 8.5 - - + +
530B ILE* 3.6 43.7 - - + +
532B LYS 5.8 2.2 - - - +
539B ILE 4.7 1.7 + - - +
541B LEU* 3.8 32.5 - - + +
548B LEU* 4.7 6.5 - - + -
556B ILE* 4.2 24.2 - - + -
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Residues in contact with LYS 503 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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501B THR* 3.3 8.8 + - - +
502B ILE* 1.3 78.9 - - - +
504B GLU* 1.3 53.6 + - + +
506B ILE* 3.2 1.2 + - - +
507B ILE* 2.8 53.4 + - + +
512B TYR* 3.6 35.6 + - + -
517B TYR* 3.5 32.8 + - + +
518B ARG* 4.3 9.6 - - - +
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Residues in contact with GLU 504 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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498B MET* 4.1 11.9 - - + +
499B PRO 5.4 0.9 - - - +
500B GLY* 3.6 12.5 - - - -
501B THR* 3.0 41.8 + - - +
503B LYS* 1.3 76.5 - - + +
505B ASN* 1.3 57.9 + - - +
507B ILE* 4.6 4.7 - - - -
508B ALA* 2.9 27.7 + - - +
532E LYS* 4.6 17.5 + - + +
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Residues in contact with ASN 505 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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497B ILE* 3.5 8.2 - - - -
498B MET* 2.6 58.4 + - - +
499B PRO 4.5 0.6 + - - -
500B GLY* 3.9 4.2 + - - -
501B THR 3.0 25.2 + - - +
502B ILE* 3.5 7.2 - - - +
503B LYS 3.2 0.2 - - - -
504B GLU* 1.3 78.5 - - - +
506B ILE* 1.3 59.3 + - - +
508B ALA* 3.6 3.1 - - - +
541B LEU* 3.7 12.4 - - + +
556B ILE* 4.0 12.6 - - + -
560B ARG* 2.6 49.6 + - - +
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Residues in contact with ILE 506 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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502B ILE* 3.0 37.9 + - + +
503B LYS 3.8 2.5 - - - +
505B ASN* 1.3 77.5 - - - +
507B ILE* 1.3 64.9 + - - +
517B TYR* 3.8 24.5 - - + +
520B VAL* 4.9 2.2 - - + -
521B ILE* 3.6 27.4 - - + -
526B LEU* 4.4 9.0 - - + -
530B ILE* 3.8 4.5 - - + -
556B ILE* 4.2 11.7 - - + +
559B ALA* 4.0 21.5 - - + +
560B ARG* 3.5 23.2 - - - +
563B TYR* 4.0 26.3 - - + -
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Residues in contact with ILE 507 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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503B LYS* 2.8 32.7 + - + +
504B GLU* 4.4 3.6 - - - +
506B ILE* 1.3 73.2 - - - +
508B ALA* 1.3 66.3 + - - +
509B GLY 4.4 3.1 - - - +
510B VAL* 2.9 55.4 + - - +
511B SER 4.7 0.2 - - - -
512B TYR* 3.6 33.4 - - + +
517B TYR* 3.7 15.9 - - + -
563B TYR* 3.4 34.5 - - + +
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Residues in contact with ALA 508 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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498B MET* 4.3 10.1 - - - -
504B GLU 2.9 18.0 + - - +
505B ASN 3.6 18.2 - - - +
507B ILE* 1.3 78.0 - - - +
509B GLY* 1.3 52.6 + - - +
510B VAL* 3.4 1.6 + - - +
560B ARG* 3.7 23.8 - - + +
670E SER* 2.7 34.2 - - - +
671E LEU 3.6 15.9 - - - +
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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