Contacts of the strand formed by residues 484 - 489 (chain C) in PDB entry 5MNJ
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 MET 484 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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451C VAL* 2.9 39.8 + - + +
469C LYS* 3.9 13.7 - - - +
482C ILE* 3.5 2.9 - - - +
483C GLN* 1.3 89.5 - - + +
485C ILE* 1.3 73.6 + - - +
486C VAL* 3.8 25.1 - - + -
450D ILE* 4.9 3.8 - - + -
452D GLY 4.4 15.7 - - - +
453D ARG* 5.3 2.7 - - - -
483D LEU* 4.3 23.8 - - + -
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Residues in contact with ILE 485 (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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449C CYS 3.4 9.6 - - - +
450C ILE* 4.0 18.4 - - + -
462C PHE* 3.5 36.7 - - + -
465C ALA* 3.7 40.2 - - + +
466C LYS* 4.2 8.1 - - + +
469C LYS* 3.8 17.5 - - + +
482C ILE* 3.5 21.1 - - + -
484C MET* 1.3 85.9 - - - +
486C VAL* 1.3 64.3 + - - +
453D ARG* 4.0 12.8 - - - +
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Residues in contact with VAL 486 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
447C ASN 3.5 0.5 - - - +
448C GLY* 3.8 0.5 - - - -
449C CYS* 2.9 35.3 + - + +
451C VAL* 3.4 27.4 - - + -
462C PHE* 4.2 2.2 - - - -
484C MET* 3.8 16.8 - - - -
485C ILE* 1.3 76.5 - - - +
487C LEU* 1.3 60.8 + - - +
488C THR* 3.3 11.8 + - - +
448D ASN* 4.2 1.3 - - - +
450D ILE* 3.6 23.1 - - + -
453D ARG 3.5 4.9 - - - +
454D THR* 3.3 36.1 - - - +
455D GLY* 3.6 9.2 - - - +
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Residues in contact with LEU 487 (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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447C ASN* 3.6 35.0 - - + +
462C PHE* 3.8 40.4 - - + -
486C VAL* 1.3 70.1 - - - +
488C THR* 1.3 61.3 + - - +
489C TYR* 3.3 36.4 - - + +
453D ARG 2.9 13.7 + - - +
454D THR* 3.3 14.6 - - + +
455D GLY 3.3 19.4 + - - +
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Residues in contact with THR 488 (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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447C ASN* 2.8 36.9 + - - +
449C CYS* 3.4 8.6 - - - +
458C LEU* 4.7 4.3 - - + -
486C VAL* 3.3 14.0 + - - +
487C LEU* 1.3 72.1 - - - +
489C TYR* 1.3 70.2 + - - +
490C PHE* 3.5 33.2 - - + -
448D ASN* 3.2 27.9 + - - +
455D GLY 3.5 4.5 - - - +
457D LEU* 4.0 19.3 - - + -
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Residues in contact with TYR 489 (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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447C ASN* 6.3 0.7 - - - -
487C LEU* 3.3 41.0 - - + +
488C THR* 1.3 74.5 - - - +
490C PHE* 1.3 67.2 + - - +
491C PRO* 3.6 4.8 - - + +
454D THR* 4.1 18.5 - - + +
455D GLY 2.9 16.5 + - - -
456D HIS* 3.6 31.9 - + + +
457D LEU 2.9 25.3 + - - -
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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