Contacts of the strand formed by residues 441 - 448 (chain A) in PDB entry 1XMJ
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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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397A VAL 5.9 0.2 - - - -
398A THR* 3.3 8.1 - - - +
399A ALA* 2.9 31.9 + - + +
439A PRO* 3.8 3.3 - - - +
440A VAL* 1.3 93.2 - - + +
442A LYS* 1.3 60.3 + - - +
444A ILE* 3.9 22.7 - - + -
463A GLY* 3.7 18.8 - - - +
466A SER* 3.8 12.1 - - - +
467A LEU* 3.5 38.1 - - + +
470A MET* 4.4 17.0 - - - -
475A LEU* 4.5 1.8 - - + -
619A LEU* 4.1 13.7 - - + -
622A GLY* 3.5 14.6 - - - +
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Residues in contact with LYS 442 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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397A VAL 3.9 0.2 - - - -
398A THR* 3.7 10.2 - - + +
439A PRO* 3.6 33.9 - - + +
441A LEU* 1.3 76.6 - - - +
443A ASP* 1.3 80.2 + - + +
444A ILE* 3.3 13.4 + - - +
621A GLU 5.4 3.1 - - - +
622A GLY* 2.9 19.2 + - - +
623A SER* 3.8 19.3 - - - -
624A SER 4.6 0.5 + - - -
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Residues in contact with ASP 443 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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396A ASN* 2.7 34.0 + - - +
397A VAL 2.8 13.1 + - - -
398A THR* 3.1 9.4 + - - -
442A LYS* 1.3 83.0 - - + +
444A ILE* 1.3 59.3 + - - +
445A ASN* 3.0 21.1 + - - +
623A SER* 5.8 2.0 - - - -
624A SER* 5.3 4.7 + - - -
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Residues in contact with ILE 444 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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394A MET* 3.7 29.7 - - + +
395A GLU 3.7 2.1 - - - -
396A ASN 3.2 6.2 + - - -
397A VAL* 2.8 41.8 + - + +
441A LEU* 3.9 24.7 - - + -
442A LYS 3.6 10.1 - - - +
443A ASP* 1.3 72.1 - - - +
445A ASN* 1.3 61.4 + - - +
446A PHE* 3.7 20.2 - - + -
467A LEU* 4.2 8.1 - - + -
470A MET* 6.1 0.4 - - + -
617A LEU* 5.2 5.4 - - + -
619A LEU* 4.2 15.7 - - + -
622A GLY 3.4 24.5 - - - +
624A SER* 4.2 12.1 - - - +
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Residues in contact with ASN 445 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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394A MET 3.3 3.7 - - - +
395A GLU* 3.3 10.2 - - - +
396A ASN* 2.6 32.8 + - - +
443A ASP* 3.0 39.2 + - - +
444A ILE* 1.3 72.9 - - - +
446A PHE* 1.3 65.5 + - - +
617A LEU* 6.0 0.9 - - - +
624A SER* 5.5 6.6 + - - -
627A TYR* 4.0 15.4 - - - +
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Residues in contact with PHE 446 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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392A VAL* 4.1 20.0 - - + -
393A VAL* 4.7 0.5 - - - +
394A MET* 2.8 74.0 + - + +
444A ILE* 3.7 17.3 - - + -
445A ASN* 1.3 73.8 - - - +
447A LYS* 1.3 70.3 + - - +
448A ILE* 4.2 10.5 - - + -
454A LEU* 4.1 26.0 - - + -
467A LEU* 4.2 17.3 - - + -
471A ILE* 4.9 6.5 - - + -
601A ILE* 5.1 1.8 - - + -
617A LEU* 4.8 10.8 - - + -
627A TYR* 3.4 31.9 - + + -
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Residues in contact with LYS 447 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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391A GLU* 4.9 4.9 - - - -
392A VAL 3.5 3.6 - - - +
393A VAL* 3.8 28.9 - - + +
446A PHE* 1.3 77.6 - - - +
448A ILE* 1.3 64.6 + - - +
449A GLU* 3.5 36.2 + - - +
452A GLN* 4.5 3.8 - - - +
615A LYS* 5.4 2.6 + - - +
627A TYR* 2.7 24.6 + - - +
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Residues in contact with ILE 448 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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391A GLU* 3.4 6.6 - - - +
392A VAL* 2.9 58.5 + - + +
446A PHE* 4.2 13.9 - - + -
447A LYS* 1.3 75.0 - - - +
449A GLU* 1.3 68.8 + - - +
452A GLN* 3.6 37.0 - - + +
453A LEU 3.9 2.5 - - - +
454A LEU* 3.6 39.5 - - + +
599A THR* 4.2 9.6 - - + -
600A ARG 5.2 1.1 - - - +
601A ILE* 5.4 7.4 - - + -
615A LYS* 4.8 9.2 - - + +
627A TYR* 5.7 0.7 - - + +
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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