Contacts of the strand formed by residues 417 - 422 (chain C) in PDB entry 1MPX
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 417 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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415C THR 3.9 10.3 - - - +
416C SER* 1.3 77.2 - - - +
418C PRO* 1.3 70.5 - - + +
419C LEU 3.4 1.4 + - - -
429C PHE* 4.0 24.8 - - + -
633C SER* 4.7 1.1 - - - -
634C LEU* 3.0 31.4 + - - +
636C VAL* 4.1 31.9 - - + +
637C ARG 6.1 1.0 - - - -
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Residues in contact with PRO 418 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
416C SER 4.2 4.5 - - - +
417C LYS* 1.3 83.8 - - + +
419C LEU* 1.3 58.4 + - - +
420C TYR* 3.7 33.3 - - + +
429C PHE* 3.4 25.4 - - - +
631C TYR* 3.6 27.8 - - + -
632C ILE 3.7 5.6 - - - +
633C SER* 4.6 1.8 - - - -
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Residues in contact with LEU 419 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
417C LYS 3.4 0.2 + - - -
418C PRO* 1.3 71.0 - - - +
420C TYR* 1.3 60.0 + - - +
421C LEU* 3.8 4.7 + - - +
427C LEU* 3.8 33.9 - - + -
428C SER* 3.7 24.5 - - - +
429C PHE* 3.7 33.7 - - + -
487C THR* 5.0 6.5 - - + -
494C LEU* 5.8 0.4 - - + -
519C LEU* 4.8 2.0 - - + -
584C VAL* 3.9 19.1 - - + -
586C VAL* 4.8 6.7 - - + -
631C TYR* 3.3 4.2 - - - -
632C ILE* 2.9 40.9 + - + +
634C LEU* 4.3 19.5 - - + -
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Residues in contact with TYR 420 (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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418C PRO* 3.7 34.7 - - + +
419C LEU* 1.3 72.3 - - - +
421C LEU* 1.3 66.6 + - - +
422C GLN* 3.5 16.3 - - - +
427C LEU* 3.3 7.0 - - - +
428C SER 2.8 32.5 + - - +
429C PHE 3.8 11.0 - - - -
430C GLN 3.5 16.4 - - - -
431C PRO* 3.6 27.2 - - + +
432C PRO* 3.7 19.1 - - + -
629C PRO* 3.9 25.1 - - + -
630C SER 3.7 3.1 - - - -
631C TYR* 3.7 24.9 - + + -
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Residues in contact with LEU 421 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
419C LEU 4.0 7.6 - - - +
420C TYR* 1.3 75.9 - - - +
422C GLN* 1.3 63.7 + - - +
426C LYS 4.1 0.7 - - - -
427C LEU* 3.8 19.7 - - + -
432C PRO* 4.7 1.6 - - - +
485C PHE* 3.6 37.0 - - + -
504C LEU* 4.8 4.0 - - + -
586C VAL* 4.5 14.6 - - + -
588C VAL* 4.3 11.4 - - + -
622C VAL* 3.9 18.4 - - + -
624C VAL* 3.3 30.7 - - + +
630C SER* 3.1 24.8 + - - +
631C TYR* 4.1 9.2 - - - -
632C ILE* 4.7 5.2 - - + -
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Residues in contact with GLN 422 (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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420C TYR* 3.5 19.4 - - - +
421C LEU* 1.3 80.7 - - - +
423C ALA* 1.3 66.9 + - - +
425C GLY 3.4 0.3 + - - -
426C LYS* 2.9 41.3 + - + +
427C LEU* 4.1 4.3 - - - +
428C SER* 3.2 15.3 + - - +
430C GLN* 2.7 30.1 + - - +
431C PRO 4.1 1.2 + - - -
432C PRO* 3.5 26.1 - - - +
436C GLN* 4.8 8.3 + - - +
485C PHE* 3.3 19.3 - - - -
624C VAL* 4.1 6.5 - - - +
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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