Contacts of the strand formed by residues 441 - 448 (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 441 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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397B VAL 4.2 1.1 - - - +
398B THR* 3.2 7.8 - - - +
399B ALA* 2.9 31.7 + - + +
439B PRO* 3.7 2.3 - - - +
440B VAL* 1.3 92.6 - - + +
442B LYS* 1.3 61.6 + - - +
444B ILE* 4.0 16.8 - - + -
463B GLY* 3.6 24.2 - - - +
466B SER 4.0 5.2 - - - -
467B LEU* 3.6 29.6 - - + +
470B MET* 3.5 30.1 - - + -
475B LEU* 4.0 9.4 - - + -
619B LEU* 4.3 12.1 - - + -
622B GLY* 3.4 12.6 - - - +
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Residues in contact with LYS 442 (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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397B VAL 3.5 0.6 + - - -
398B THR* 3.9 10.3 - - + +
439B PRO* 3.8 27.4 - - + +
441B LEU* 1.3 73.7 - - - +
443B ASP* 1.3 81.2 + - - +
444B ILE* 3.3 6.7 + - - +
621B GLU 5.7 0.7 - - - +
622B GLY* 2.8 17.2 + - - +
623B SER* 3.8 27.9 + - - +
624B SER 4.4 1.0 + - - -
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Residues in contact with ASP 443 (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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396B ASN* 2.8 35.0 + - - +
397B VAL 2.8 15.2 + - - +
398B THR* 3.3 9.6 + - - +
442B LYS* 1.3 84.8 - - + +
444B ILE* 1.3 58.8 + - - +
445B ASN* 3.2 17.2 + - - -
624B SER* 4.7 8.0 + - - -
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Residues in contact with ILE 444 (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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394B MET* 3.6 17.6 - - - +
396B ASN 3.3 6.8 + - - -
397B VAL* 3.0 34.7 + - + +
441B LEU* 4.0 28.7 - - + -
442B LYS 3.7 6.1 - - - +
443B ASP* 1.3 74.7 - - - +
445B ASN* 1.3 62.3 + - - +
446B PHE* 3.7 32.3 - - + -
467B LEU* 4.2 5.6 - - + -
470B MET* 5.3 0.4 - - + -
617B LEU* 4.7 5.8 - - + -
619B LEU* 3.9 22.9 - - + -
622B GLY 3.4 22.4 - - - +
624B SER* 4.1 13.2 - - - +
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Residues in contact with ASN 445 (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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394B MET 3.3 4.7 - - - +
395B GLU* 3.5 6.8 - - - +
396B ASN* 2.6 35.2 + - - +
443B ASP* 3.2 42.0 + - - -
444B ILE* 1.3 75.2 - - - +
446B PHE* 1.3 66.4 + - - +
617B LEU* 5.3 2.3 - - - +
624B SER* 4.9 9.4 + - - -
627B TYR* 4.1 17.3 - - - +
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Residues in contact with PHE 446 (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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392B VAL* 3.8 29.2 - - + -
393B VAL* 3.6 2.9 - - - +
394B MET* 2.9 72.6 + - + +
444B ILE* 3.7 18.6 - - + -
445B ASN* 1.3 74.5 - - - +
447B LYS* 1.3 69.8 + - - +
448B ILE* 4.5 2.5 - - + -
454B LEU* 4.2 25.6 - - + -
467B LEU* 3.9 18.2 - - + -
471B ILE* 4.7 6.5 - - + -
601B ILE* 4.8 3.1 - - + -
617B LEU* 3.9 13.9 - - + -
627B TYR* 3.7 28.3 - - + -
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Residues in contact with LYS 447 (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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391B GLU* 3.0 34.3 + - - +
392B VAL 3.4 3.4 - - - -
393B VAL* 4.3 22.4 - - + +
446B PHE* 1.3 79.1 - - - +
448B ILE* 1.3 68.6 + - - +
449B GLU* 3.7 30.4 + - - +
452B GLN* 5.0 0.9 - - - +
615B LYS* 4.7 5.4 + - - +
627B TYR* 2.7 28.9 + - + +
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Residues in contact with ILE 448 (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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391B GLU* 3.3 6.9 - - - +
392B VAL* 2.9 57.9 + - + +
446B PHE* 4.5 6.2 - - + -
447B LYS* 1.3 75.0 - - - +
449B GLU* 1.3 65.9 + - - +
452B GLN* 3.7 38.8 - - + +
453B LEU 3.8 10.5 - - - +
454B LEU* 3.7 38.1 - - + -
599B THR* 3.8 11.9 - - + -
600B ARG 5.1 0.4 - - - +
601B ILE* 5.2 5.2 - - + -
615B LYS* 4.0 16.4 - - + +
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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