Contacts of the helix formed by residues 502 - 508 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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501E THR* 1.3 76.8 + - - +
503E LYS* 1.3 61.5 + - - +
505E ASN* 3.2 5.7 + - - +
506E ILE* 3.0 43.5 + - + +
526E LEU* 5.3 3.6 - - + -
529E ASP* 5.0 4.3 - - + +
530E ILE* 4.4 23.3 - - + -
533E PHE* 3.9 30.3 - - + -
536E LYS 4.5 5.2 - - - +
537E ASP 4.4 3.4 - - - +
539E ILE* 3.9 15.9 + - + -
541E LEU* 3.7 28.7 - - + +
548E LEU* 5.4 2.7 - - + -
556E ILE* 4.0 25.4 - - + -
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Residues in contact with LYS 503 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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501E THR* 3.3 4.0 - - + -
502E ILE* 1.3 78.2 - - - +
504E GLU* 1.3 60.9 + - + +
506E ILE* 3.2 2.6 + - - +
507E ILE* 2.8 44.7 + - + +
512E TYR* 3.8 35.3 + - + -
517E TYR* 3.5 28.4 + - + +
537E ASP* 3.4 31.9 + - + +
538E ASN* 3.8 22.0 + - - +
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Residues in contact with GLU 504 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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498E MET* 3.6 9.4 - - + +
499E PRO 5.3 1.6 - - - +
500E GLY* 4.3 8.7 - - - -
501E THR* 3.3 34.3 + - + +
503E LYS* 1.3 84.1 - - + +
505E ASN* 1.3 56.9 + - - +
507E ILE* 4.4 6.5 - - + -
508E ALA* 2.8 30.0 + - - -
540E VAL* 6.0 0.7 - - - +
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Residues in contact with ASN 505 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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497E ILE* 3.5 8.8 - - - +
498E MET* 2.7 56.5 + - - +
500E GLY* 3.6 12.5 + - - -
501E THR 2.8 27.8 + - - +
502E ILE* 3.2 8.3 + - - +
504E GLU* 1.3 75.6 - - - +
506E ILE* 1.3 59.1 + - - +
508E ALA* 3.7 3.3 - - - +
541E LEU* 3.8 8.7 - - - +
556E ILE* 4.0 15.3 - - + -
560E ARG* 2.8 46.4 + - - +
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Residues in contact with ILE 506 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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502E ILE* 3.0 37.7 + - + +
503E LYS 3.7 2.7 - - - +
505E ASN* 1.3 75.9 - - - +
507E ILE* 1.3 66.1 + - - +
517E TYR* 3.8 33.7 - - + +
520E VAL* 4.5 4.5 - - + -
521E ILE* 4.1 7.2 - - + -
526E LEU* 4.1 20.9 - - + -
530E ILE* 5.2 0.2 - - + -
556E ILE* 4.1 12.1 - - + +
559E ALA* 3.9 31.9 - - + +
560E ARG* 3.5 22.8 - - - +
563E TYR* 4.0 18.4 - - + +
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Residues in contact with ILE 507 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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503E LYS* 2.8 33.7 + - + +
504E GLU* 4.1 5.6 - - + +
506E ILE* 1.3 74.7 - - - +
508E ALA* 1.3 64.5 + - - +
509E GLY 4.2 4.7 - - - +
510E VAL* 3.0 51.5 - - + +
512E TYR* 3.6 32.5 - - + +
517E TYR* 3.7 17.5 - - + -
563E TYR* 3.4 33.9 - - + +
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Residues in contact with ALA 508 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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496E TRP* 6.1 0.4 - - + -
498E MET* 4.0 18.8 - - + -
504E GLU 2.8 20.3 + - - +
505E ASN 3.7 16.2 - - - +
507E ILE* 1.3 74.8 - - - +
509E GLY* 1.3 55.9 + - - +
510E VAL* 3.4 6.4 + - - +
560E ARG* 3.9 21.1 - - + -
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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