Contacts of the strand formed by residues 453 - 458 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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448C ILE* 3.7 3.8 - - - +
452C GLN* 1.3 71.4 - - - +
454C LEU* 1.3 71.5 + - - +
455C ALA* 5.3 1.3 - - + -
587C PHE* 4.2 25.4 - - + -
591C VAL* 4.2 11.9 - - + -
592C CYS* 5.0 1.3 - - - -
600C ARG* 3.5 42.5 - - + +
602C LEU* 4.0 20.2 - - + -
609C HIS 4.7 0.7 - - - +
612C LYS* 4.4 7.6 - - + +
613C ALA* 3.6 28.4 - - + +
614C ASP* 2.9 40.8 + - - +
615C LYS 3.3 8.5 + - - +
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Residues in contact with LEU 454 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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446C PHE* 3.8 35.9 - - + -
447C LYS 5.5 0.4 - - - +
448C ILE* 3.6 23.3 - - + +
453C LEU* 1.3 75.2 - - - +
455C ALA* 1.3 75.5 + - - +
456C VAL* 3.9 20.5 + - + -
467C LEU* 5.5 0.7 - - + -
600C ARG 2.8 13.9 + - - +
601C ILE* 3.4 17.9 - - + +
602C LEU* 2.8 26.9 + - - +
615C LYS* 3.4 26.5 - - + +
616C ILE 3.8 1.8 - - - -
617C LEU* 3.8 17.3 - - + +
627C TYR* 5.2 2.9 - - + -
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Residues in contact with ALA 455 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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453C LEU* 5.4 1.1 - - + -
454C LEU* 1.3 73.5 - - - +
456C VAL* 1.3 61.9 + - - +
457C ALA 4.1 0.8 + - - -
602C LEU* 3.3 7.6 - - + +
604C THR* 4.1 10.3 - - + -
609C HIS* 4.4 2.7 - - + +
610C LEU* 3.9 27.0 - - + +
613C ALA* 3.7 22.1 - - + +
615C LYS 3.0 9.0 + - - +
616C ILE* 3.3 6.7 - - + +
617C LEU 2.8 26.7 + - - +
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Residues in contact with VAL 456 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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454C LEU* 3.9 15.0 - - + -
455C ALA* 1.3 75.1 - - - +
457C ALA* 1.3 63.2 + - - +
464C LYS* 3.8 30.1 - - + -
467C LEU* 4.3 13.5 - - + -
468C LEU* 5.4 0.2 - - + -
601C ILE* 3.7 27.8 - - + -
602C LEU 2.8 12.0 + - - +
603C VAL* 3.3 15.8 - - + +
604C THR* 3.0 25.4 + - - +
617C LEU* 3.4 15.5 - - + +
619C LEU* 4.2 14.4 - - + -
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Residues in contact with ALA 457 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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455C ALA 4.1 0.8 + - - -
456C VAL* 1.3 72.8 - - - +
458C GLY* 1.3 59.1 + - - +
464C LYS* 3.7 7.7 - - - +
604C THR 3.3 19.7 - - - +
605C SER* 5.0 1.6 - - - -
610C LEU* 4.3 14.6 - - + -
617C LEU 3.0 7.1 + - - +
618C ILE* 3.4 23.9 - - + -
619C LEU* 2.8 28.2 + - - +
645C MET* 3.7 15.7 - - + +
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Residues in contact with GLY 458 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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457C ALA* 1.3 74.7 - - - +
459C SER* 1.3 61.7 + - - -
462C ALA* 4.3 1.6 - - - -
464C LYS* 2.7 26.8 + - - +
618C ILE* 5.0 0.4 - - - -
619C LEU 3.4 12.3 - - - -
644C LEU 3.2 14.1 - - - -
645C MET 3.1 9.7 + - - +
646C GLY* 3.1 17.0 - - - +
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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