Contacts of the strand formed by residues 615 - 620 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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447E LYS 4.7 6.4 + - - +
448E ILE* 4.1 16.2 - - + -
449E GLU* 6.2 1.0 - - - +
452E GLN* 4.7 11.0 + - - +
453E LEU 3.3 2.6 + - - -
454E LEU* 3.3 17.4 - - + +
455E ALA 3.0 22.5 + - - -
613E ALA* 3.4 6.2 - - - +
614E ASP* 1.3 87.1 - - - +
616E ILE* 1.3 64.0 + - - +
627E TYR* 4.0 34.5 + - + +
628E GLY* 3.7 19.5 - - - -
629E THR* 4.5 11.0 - - - +
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Residues in contact with ILE 616 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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454E LEU* 3.9 2.7 - - - -
455E ALA* 3.3 9.9 - - + +
610E LEU* 3.6 44.4 - - + +
613E ALA* 4.0 7.2 - - + +
615E LYS* 1.3 80.1 - - - +
617E LEU* 1.3 59.9 + - - +
618E ILE* 3.8 19.3 - - + -
626E PHE* 3.6 26.9 - - + +
627E TYR* 3.4 7.8 - - - -
628E GLY 2.7 44.8 + - - +
629E THR 4.3 3.8 - - - +
630E PHE* 4.6 7.6 - - - +
633E LEU* 3.6 27.1 - - + -
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Residues in contact with LEU 617 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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444E ILE* 4.7 5.4 - - + -
445E ASN 5.2 3.4 - - - +
446E PHE* 4.3 20.0 - - + -
454E LEU* 3.9 14.6 - - + +
455E ALA 2.8 10.1 + - - +
456E VAL* 3.3 10.7 - - + +
457E ALA 2.9 26.0 + - - +
467E LEU* 3.9 25.8 - - + -
616E ILE* 1.3 74.8 - - - +
618E ILE* 1.3 70.8 + - - +
619E LEU* 3.9 22.4 - - + -
624E SER* 3.6 24.2 - - - +
626E PHE 3.4 13.7 - - - +
627E TYR* 4.4 13.7 - - + -
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Residues in contact with ILE 618 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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455E ALA 5.9 0.2 - - - +
457E ALA* 3.3 31.6 - - + +
610E LEU* 4.7 2.7 - - + -
616E ILE* 3.8 26.7 - - + -
617E LEU* 1.3 74.5 - - - +
619E LEU* 1.3 68.2 + - - +
624E SER* 3.7 4.2 - - - -
625E TYR* 2.8 48.3 + - + -
626E PHE* 2.8 35.0 + - + +
633E LEU* 4.5 4.5 - - + -
644E LEU* 4.6 16.8 - - + +
645E MET* 3.8 20.4 - - + -
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Residues in contact with LEU 619 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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441E LEU* 4.4 9.9 - - + -
444E ILE* 3.9 21.3 - - + -
456E VAL* 3.8 26.7 - - + -
457E ALA 2.8 10.1 + - - +
458E GLY* 3.4 19.4 - - - -
459E SER 4.3 0.2 + - - -
462E ALA* 3.8 25.3 - - + +
463E GLY 3.8 26.7 - - - +
464E LYS* 3.9 3.1 - - + +
467E LEU* 4.5 5.2 - - + -
617E LEU* 3.9 26.4 + - + -
618E ILE* 1.3 81.0 - - - +
620E HIS* 1.3 65.2 + - - +
622E GLY 4.9 1.1 - - - -
623E SER 3.4 13.2 - - - +
625E TYR* 4.5 0.4 - - - -
644E LEU* 4.5 1.4 - - - +
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Residues in contact with HIS 620 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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459E SER* 3.8 22.2 + - - -
462E ALA* 4.2 1.6 - - - -
618E ILE 4.2 0.2 + - - -
619E LEU* 1.3 76.0 + - - +
621E GLU* 1.3 96.9 + - + +
623E SER* 2.9 25.8 + - - +
625E TYR* 4.2 24.0 - + + -
644E LEU* 4.2 24.4 + - + +
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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