Contacts of the strand formed by residues 494 - 498 (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 LEU 494 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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419C LEU* 5.8 0.4 - - + -
429C PHE* 3.8 31.9 - - + -
490C LEU* 4.1 21.8 - - + -
492C GLU 3.5 1.7 + - - +
493C PRO* 1.3 71.1 - - - +
495C GLN* 1.3 58.9 + - - +
496C ILE* 4.6 4.9 - - + -
577C THR* 3.4 1.6 - - - -
578C PHE* 2.8 46.4 + - + +
584C VAL* 4.0 26.0 - - + -
634C LEU* 4.4 9.9 - - + -
636C VAL* 3.8 34.5 - - + -
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Residues in contact with GLN 495 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
392C ASN* 4.0 12.3 + - - +
395C GLU* 4.0 12.5 + - - +
399C ASP* 5.1 1.9 - - - +
406C ARG* 4.1 7.8 + - - -
493C PRO* 4.0 2.7 + - + +
494C LEU* 1.3 75.1 - - - +
496C ILE* 1.3 68.5 + - - +
497C ALA* 5.3 0.4 - - + -
575C ASN* 4.8 4.6 - - - +
576C HIS 3.8 2.9 - - - +
577C THR* 3.4 21.9 - - + +
636C VAL* 3.4 6.4 - - - +
637C ARG* 3.0 80.6 + - + +
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Residues in contact with ILE 496 (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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494C LEU* 4.6 2.9 - - + -
495C GLN* 1.3 81.1 - - - +
497C ALA* 1.3 62.9 + - - +
500C PRO* 4.7 4.9 - - + -
519C LEU* 3.9 26.0 - - + -
540C VAL* 4.8 0.9 - - + -
574C ALA* 3.4 25.3 - - + +
575C ASN* 3.5 2.1 - - - +
576C HIS* 3.1 48.8 + - + +
578C PHE* 3.9 21.8 - - + -
634C LEU* 3.7 33.9 - - + -
635C PRO* 3.2 14.4 - - + +
636C VAL* 4.3 7.2 - - + -
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Residues in contact with ALA 497 (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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404C TRP* 3.5 26.0 - - + -
406C ARG* 3.2 27.9 + - + -
407C SER 3.2 21.7 + - - -
495C GLN* 5.3 1.1 - - + -
496C ILE* 1.3 75.9 - - - +
498C GLY* 1.3 58.0 + - - +
574C ALA 3.2 6.3 - - - -
575C ASN* 3.7 8.3 - - - +
635C PRO* 2.8 12.3 + - - +
637C ARG* 4.2 12.3 - - + +
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Residues in contact with GLY 498 (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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404C TRP* 3.6 5.8 - - - -
405C PRO* 3.7 18.2 - - - -
407C SER 3.9 0.4 - - - -
497C ALA* 1.3 76.7 - - - +
499C ALA* 1.3 61.5 + - - -
500C PRO* 3.4 4.7 - - - +
573C THR* 3.5 5.6 - - - -
574C ALA 2.9 31.2 + - - +
635C PRO* 3.5 15.6 - - - +
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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