Contacts of the strand formed by residues 441 - 448 (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 441 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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397C VAL 4.2 1.1 - - - +
398C THR* 3.2 8.0 - - - +
399C ALA* 2.8 33.5 + - + +
439C PRO* 3.6 2.5 - - - +
440C VAL* 1.3 89.4 - - + +
442C LYS* 1.3 60.1 - - - +
444C ILE* 3.9 22.0 - - + -
463C GLY 3.6 21.5 - - - +
466C SER* 4.0 1.1 - - - -
467C LEU* 3.7 28.0 - - + +
470C MET* 3.7 27.4 - - + -
475C LEU* 4.0 16.8 - - + -
619C LEU* 4.4 8.1 - - + -
622C GLY* 3.2 17.9 - - - +
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Residues in contact with LYS 442 (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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397C VAL 3.9 0.4 - - - -
398C THR* 3.9 11.0 - - + +
439C PRO* 4.2 22.9 - - + +
441C LEU* 1.3 75.1 - - - +
443C ASP* 1.3 80.9 + - + +
444C ILE* 3.4 2.3 + - - +
621C GLU 5.6 1.1 - - - +
622C GLY* 2.7 11.2 + - - +
623C SER* 3.4 38.0 - - - +
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Residues in contact with ASP 443 (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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396C ASN* 3.2 33.6 + - - +
397C VAL 3.0 14.2 + - - +
398C THR* 3.4 10.0 + - - +
442C LYS* 1.3 84.0 - - + +
444C ILE* 1.3 58.7 + - - +
445C ASN* 3.1 20.4 + - - -
623C SER* 5.3 2.0 - - - -
624C SER* 4.0 10.4 + - - -
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Residues in contact with ILE 444 (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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394C MET* 3.8 8.3 - - + +
395C GLU 3.6 6.2 + - - -
396C ASN 3.1 19.2 + - - -
397C VAL* 2.9 31.8 + - + +
441C LEU* 3.9 30.5 - - + -
442C LYS 4.1 0.4 - - - +
443C ASP* 1.3 70.9 - - - +
445C ASN* 1.3 61.9 + - - +
446C PHE* 3.9 23.8 - - + -
467C LEU* 3.9 17.0 - - + -
470C MET* 5.2 0.7 - - + -
617C LEU* 4.9 2.9 - - + -
619C LEU* 4.0 15.9 - - + -
622C GLY 3.3 24.0 - - - +
624C SER* 3.7 17.9 - - - +
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Residues in contact with ASN 445 (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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394C MET 3.4 5.3 - - - +
395C GLU* 3.3 9.2 - - - +
396C ASN* 2.7 32.4 + - - +
443C ASP* 3.1 41.2 + - - -
444C ILE* 1.3 75.4 + - - +
446C PHE* 1.3 65.7 + - - +
617C LEU* 4.3 0.9 - - - +
624C SER* 3.2 20.8 + - - +
627C TYR* 4.1 15.2 - - - +
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Residues in contact with PHE 446 (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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392C VAL* 3.7 40.2 - - + -
393C VAL* 3.7 2.4 - - - +
394C MET* 3.1 65.8 + - + +
444C ILE* 3.9 15.3 - - + -
445C ASN* 1.3 74.3 - - - +
447C LYS* 1.3 72.1 + - - +
448C ILE* 4.6 2.7 - - + -
454C LEU* 3.8 27.4 - - + -
467C LEU* 4.0 16.2 - - + -
471C ILE* 4.7 7.6 - - + -
601C ILE* 4.7 1.3 - - + -
617C LEU* 3.9 17.3 - - + -
627C TYR* 3.7 26.5 - - + -
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Residues in contact with LYS 447 (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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391C GLU* 3.6 20.9 + - - -
392C VAL 3.3 6.1 - - - +
393C VAL* 4.1 22.9 - - + +
446C PHE* 1.3 82.0 - - - +
448C ILE* 1.3 70.2 + - - +
449C GLU* 3.3 29.7 + - + +
452C GLN* 5.0 0.3 - - - +
615C LYS* 4.1 7.3 + - - +
627C TYR* 2.6 37.8 + - + +
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Residues in contact with ILE 448 (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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391C GLU* 3.3 6.6 - - - +
392C VAL* 2.9 61.7 + - + -
446C PHE* 4.3 6.5 - - + -
447C LYS* 1.3 74.6 - - - +
449C GLU* 1.3 63.4 + - - +
452C GLN* 3.5 45.1 - - + +
453C LEU 3.7 6.3 - - - +
454C LEU* 3.6 40.2 - - + +
599C THR* 4.0 11.0 - - + -
600C ARG 5.0 0.2 - - - +
601C ILE* 4.8 4.7 - - + -
615C LYS* 3.8 20.4 - - + +
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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