Contacts of the strand formed by residues 453 - 457 (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 LEU 453 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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448E ILE* 3.7 4.2 - - - +
452E GLN* 1.3 71.9 - - - +
454E LEU* 1.3 68.8 + - - +
455E ALA* 4.7 1.3 - - + +
587E PHE* 4.3 24.9 - - + -
591E VAL* 4.2 12.1 - - + -
592E CYS* 5.0 2.7 - - - -
600E ARG* 3.4 43.2 - - + +
602E LEU* 3.9 23.3 - - + +
609E HIS 4.7 1.3 - - - +
612E LYS 4.3 4.3 - - - +
613E ALA* 3.7 28.0 - - + +
614E ASP* 2.9 38.2 + - - +
615E LYS 3.3 8.5 + - - +
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Residues in contact with LEU 454 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
446E PHE* 4.2 31.6 - - + -
448E ILE* 3.6 23.3 - - + +
453E LEU* 1.3 75.1 - - - +
455E ALA* 1.3 65.4 - - - +
456E VAL* 3.8 22.2 - - + -
467E LEU* 5.3 0.7 - - + -
600E ARG 2.9 11.4 + - - +
601E ILE* 3.3 19.2 - - + +
602E LEU 2.8 31.9 + - - -
615E LYS* 3.3 31.9 - - + +
616E ILE* 3.9 1.3 - - - -
617E LEU* 3.9 18.6 - - + +
627E TYR* 4.7 5.6 - - + -
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Residues in contact with ALA 455 (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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453E LEU* 4.0 3.2 + - + -
454E LEU* 1.3 73.4 - - - +
456E VAL* 1.3 62.2 + - - +
457E ALA 4.2 0.4 + - - -
602E LEU* 3.3 9.9 - - + +
604E THR* 4.1 7.2 - - + -
609E HIS* 4.3 4.5 - - + +
610E LEU* 3.8 26.4 - - + +
613E ALA* 3.7 21.3 - - + +
615E LYS 3.0 7.5 + - - -
616E ILE* 3.3 6.5 - - + +
617E LEU 2.8 27.0 + - - +
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Residues in contact with VAL 456 (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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454E LEU* 3.8 15.5 - - + -
455E ALA* 1.3 75.5 - - - +
457E ALA* 1.3 63.0 + - - +
464E LYS* 4.1 17.3 - - + +
467E LEU* 4.3 14.1 - - + -
468E LEU* 5.6 0.2 - - + -
601E ILE* 3.7 28.9 - - + -
602E LEU 2.8 13.1 + - - +
603E VAL* 3.3 16.1 - - + +
604E THR* 2.9 28.2 + - - +
617E LEU* 3.3 11.2 - - + +
619E LEU* 3.8 28.7 - - + -
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Residues in contact with ALA 457 (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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455E ALA 4.2 0.4 + - - -
456E VAL* 1.3 73.6 - - - +
458E GLY* 1.3 54.5 + - - +
464E LYS* 3.6 7.9 - - - +
604E THR 3.3 18.8 - - - +
605E SER* 5.1 1.3 - - - -
610E LEU* 4.5 12.6 - - + -
617E LEU 2.9 6.3 + - - +
618E ILE* 3.3 26.6 - - + -
619E LEU* 2.8 34.0 + - - +
645E MET* 3.9 15.0 - - + +
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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