Contacts of the strand formed by residues 453 - 457 (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 LEU 453 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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448B ILE* 3.8 2.5 - - - +
452B GLN* 1.3 72.3 - - - +
454B LEU* 1.3 65.7 + - - +
455B ALA* 4.6 1.3 - - + +
587B PHE* 4.4 16.6 - - + -
591B VAL* 4.3 21.3 - - + -
592B CYS* 5.3 2.2 - - - -
600B ARG* 3.4 41.7 - - + +
602B LEU* 3.8 29.4 - - + -
609B HIS 4.7 1.6 - - - +
612B LYS* 4.5 4.7 - - + +
613B ALA* 3.7 26.9 - - + +
614B ASP* 2.8 39.2 + - - +
615B LYS 3.3 8.7 + - - +
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Residues in contact with LEU 454 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
446B PHE* 4.2 32.3 - - + -
447B LYS 6.4 0.2 - - - -
448B ILE* 3.7 22.1 - - + +
453B LEU* 1.3 74.3 - - - +
455B ALA* 1.3 72.6 + - - +
456B VAL* 3.8 21.4 + - + -
467B LEU* 5.5 0.4 - - + -
600B ARG 2.8 14.3 + - - +
601B ILE* 3.3 18.0 - - + +
602B LEU 2.8 27.4 + - - -
615B LYS* 3.3 25.1 - - + +
616B ILE 3.8 1.3 - - - -
617B LEU* 3.6 22.4 - - + +
627B TYR* 4.8 5.2 - - + -
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Residues in contact with ALA 455 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
453B LEU* 5.4 1.6 - - + -
454B LEU* 1.3 73.0 - - - +
456B VAL* 1.3 56.4 + - - +
457B ALA* 4.1 1.0 + - - -
602B LEU* 3.3 11.2 - - + +
604B THR* 4.1 17.7 - - + -
609B HIS* 4.6 2.0 - - + +
610B LEU* 4.2 11.4 - - + -
613B ALA* 3.8 21.5 - - + +
615B LYS 3.0 7.7 + - - -
616B ILE* 3.3 14.4 - - + +
617B LEU 2.8 32.4 + - - +
618B ILE* 5.6 0.2 - - - +
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Residues in contact with VAL 456 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
454B LEU* 3.8 15.3 - - + -
455B ALA* 1.3 77.0 - - - +
457B ALA* 1.3 63.4 + - - +
464B LYS* 4.0 16.8 - - + +
467B LEU* 4.2 16.2 - - + -
468B LEU* 5.5 0.7 - - + -
601B ILE* 3.7 27.4 - - + -
602B LEU 2.9 9.1 + - - -
603B VAL* 3.3 18.9 - - + +
604B THR 3.1 24.2 + - - -
617B LEU* 3.3 13.0 - - + +
619B LEU* 3.9 27.8 - - + -
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Residues in contact with ALA 457 (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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455B ALA 4.1 0.6 - - - +
456B VAL* 1.3 73.5 - - - +
458B GLY* 1.3 58.7 + - - +
464B LYS* 3.6 10.6 - - - +
604B THR 3.4 19.1 - - - +
605B SER* 5.0 1.3 - - - -
610B LEU* 4.5 11.2 - - + -
617B LEU 2.9 6.9 + - - +
618B ILE* 3.4 24.2 - - + -
619B LEU* 2.9 27.2 + - - +
645B MET* 4.0 16.8 - - - +
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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