Contacts of the strand formed by residues 615 - 620 (chain A) 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 LYS 615 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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447A LYS 4.6 4.7 + - - +
448A ILE* 3.8 23.1 - - + -
449A GLU* 6.3 0.8 - - - +
452A GLN* 4.5 11.1 + - - +
453A LEU 3.3 2.0 + - - -
454A LEU* 3.3 7.5 - - + +
455A ALA 3.0 23.0 + - - -
613A ALA* 3.6 4.4 - - - +
614A ASP* 1.3 86.5 - - + +
616A ILE* 1.3 64.2 + - - +
627A TYR* 3.4 44.6 + - + +
628A GLY* 3.4 22.2 - - - +
629A THR* 4.6 9.2 - - - +
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Residues in contact with ILE 616 (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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454A LEU* 3.9 2.5 - - - -
455A ALA* 3.3 9.2 - - + +
610A LEU* 3.6 49.1 - - + +
613A ALA* 4.0 7.2 - - + +
615A LYS* 1.3 79.3 - - - +
617A LEU* 1.3 59.6 + - - +
618A ILE* 4.2 6.5 - - + -
626A PHE* 3.7 27.6 - - + -
627A TYR* 3.4 9.7 - - - -
628A GLY 2.7 43.7 + - - +
629A THR 3.9 2.0 - - - -
630A PHE* 3.8 22.2 - - - +
633A LEU* 3.8 18.8 - - + -
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Residues in contact with LEU 617 (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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444A ILE* 4.6 6.7 - - + -
445A ASN 4.9 4.3 - - - +
446A PHE* 4.4 19.7 - - + -
454A LEU* 4.1 13.0 - - + -
455A ALA 2.9 10.3 + - - +
456A VAL* 3.4 9.8 - - + +
457A ALA 3.0 25.1 + - - +
467A LEU* 3.9 26.0 - - + -
616A ILE* 1.3 74.6 - - - +
618A ILE* 1.3 70.6 + - - +
619A LEU* 3.6 27.8 + - + -
624A SER* 3.4 26.9 - - - +
626A PHE 3.4 9.4 - - - +
627A TYR* 4.2 13.5 - - + -
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Residues in contact with ILE 618 (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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455A ALA 5.7 0.4 - - - +
457A ALA* 3.4 29.6 - - + +
458A GLY* 4.9 2.0 - - - -
610A LEU* 4.2 11.7 - - + -
616A ILE* 4.4 7.4 - - + -
617A LEU* 1.3 75.2 - - - +
619A LEU* 1.3 63.6 + - - +
624A SER* 3.7 3.8 - - - -
625A TYR* 2.8 53.7 + - + -
626A PHE* 2.8 28.6 + - + +
633A LEU* 4.0 14.6 - - + -
640A PHE* 3.6 37.9 - - + -
643A LYS* 4.7 6.5 - - - +
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Residues in contact with LEU 619 (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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441A LEU* 4.3 9.6 - - + -
444A ILE* 3.9 20.4 - - + -
456A VAL* 4.0 22.0 - - + -
457A ALA 2.8 12.5 + - - +
458A GLY* 3.4 19.6 - - - -
459A SER 4.4 0.9 + - - -
462A ALA* 3.7 24.1 - - + +
463A GLY 3.8 28.7 - - - +
464A LYS* 4.0 3.1 - - + +
467A LEU* 4.6 5.2 - - + -
617A LEU* 3.6 29.5 + - + -
618A ILE* 1.3 79.5 - - - +
620A HIS* 1.3 62.6 + - - +
622A GLY 4.8 1.3 - - - -
623A SER 3.3 13.0 - - - +
624A SER* 4.3 0.2 - - - -
643A LYS* 5.5 0.9 + - - -
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Residues in contact with HIS 620 (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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459A SER* 5.0 11.3 + - - -
462A ALA* 4.5 1.6 - - - -
618A ILE 4.1 0.2 + - - -
619A LEU* 1.3 74.6 + - - +
621A GLU* 1.3 100.4 + - + +
622A GLY 3.1 0.9 - - - -
623A SER* 2.8 31.2 + - - +
625A TYR* 4.1 24.2 - + + -
643A LYS* 3.8 21.7 + - - +
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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