Contacts of the strand formed by residues 599 - 603 (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 THR 599 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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389C THR* 3.2 8.6 + - - -
390C THR 2.5 29.3 + - - +
392C VAL* 4.4 2.7 - - + -
448C ILE* 4.0 24.9 - - + -
449C GLU 4.0 7.0 - - - +
451C GLY* 3.0 17.2 + - - +
452C GLN 3.6 5.8 - - - +
567C ASP 3.6 15.6 + - - -
568C LEU* 3.5 19.8 - - + -
569C TYR* 3.0 26.7 + - - -
598C LYS* 1.3 71.3 - - - +
600C ARG* 1.3 62.3 + - - +
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Residues in contact with ARG 600 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
448C ILE* 5.0 0.9 - - - +
451C GLY 3.2 17.4 + - - -
452C GLN 3.0 15.2 + - - +
453C LEU* 3.5 33.3 - - + +
454C LEU* 2.8 26.7 + - - +
569C TYR* 3.4 13.2 - - + +
571C LEU* 3.9 15.0 - - + -
591C VAL* 2.7 35.5 + - + +
592C CYS* 3.7 18.4 + - - +
595C MET* 3.2 28.3 + - + -
596C ALA* 3.6 7.5 + - - +
598C LYS* 3.0 26.8 + - - -
599C THR* 1.3 74.6 - - - +
601C ILE* 1.3 66.6 + - - +
602C LEU 4.1 0.4 - - - -
614C ASP* 5.0 1.2 + - - -
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Residues in contact with ILE 601 (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* 4.4 14.8 - - + -
446C PHE* 4.7 1.8 - - + -
448C ILE* 4.8 4.5 - - + -
454C LEU* 3.4 23.8 - - + -
456C VAL* 3.7 27.8 - - + -
467C LEU* 5.4 1.8 - - + -
468C LEU* 3.9 18.5 - - + +
471C ILE* 3.7 28.7 - - + -
568C LEU* 4.1 13.5 - - + -
569C TYR 2.9 7.4 + - - +
570C LEU* 3.6 17.6 - - + -
571C LEU* 2.8 34.1 + - - +
600C ARG* 1.3 77.9 - - - +
602C LEU* 1.3 56.9 + - - +
603C VAL 4.1 0.6 + - - +
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Residues in contact with LEU 602 (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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453C LEU* 4.0 16.2 - - + -
454C LEU 2.8 9.6 + - - +
455C ALA* 3.3 7.0 - - + -
456C VAL* 2.8 24.9 + - - -
571C LEU* 3.3 32.3 - - + +
574C PRO* 3.7 21.8 - - + -
575C PHE* 4.3 8.7 - - + -
587C PHE* 3.7 36.1 - - + -
591C VAL* 4.6 7.9 - - + -
600C ARG 4.1 0.4 - - - -
601C ILE* 1.3 72.1 - - - +
603C VAL* 1.3 68.4 + - - +
604C THR* 3.5 11.8 + - + +
609C HIS* 4.0 16.6 - - + +
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Residues in contact with VAL 603 (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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456C VAL* 3.3 17.9 - - + +
464C LYS* 3.9 44.0 - - + +
468C LEU* 3.9 28.3 - - + -
493C GLN* 6.1 0.2 - - - -
571C LEU 2.8 11.0 + - - +
572C ASP* 3.5 27.6 - - - +
573C SER* 3.2 30.9 + - - +
601C ILE* 4.1 0.6 - - + -
602C LEU* 1.3 75.6 - - - +
604C THR* 1.3 63.8 + - - +
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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