Contacts of the strand formed by residues 631 - 634 (chain A) 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 TYR 631 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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418A PRO* 3.7 28.0 - - + -
419A LEU 3.3 16.2 - - - +
420A TYR* 3.7 27.4 - + + -
421A LEU* 4.2 4.5 - - - +
502A VAL* 4.6 1.0 - - - +
503A HIS* 2.8 84.4 + + + +
629A PRO* 3.5 21.1 - - + -
630A SER* 1.3 75.8 - - - +
632A ILE* 1.3 72.7 + - - +
633A SER* 4.2 9.4 - - - -
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Residues in contact with ILE 632 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
419A LEU* 2.9 36.5 + - + +
421A LEU* 4.7 6.1 - - + -
500A PRO* 3.8 28.7 - - + -
501A ASP 3.5 9.4 - - - +
502A VAL* 4.6 13.0 - - + -
517A VAL* 4.1 20.2 - - + -
519A LEU* 4.5 11.0 - - + -
571A LEU* 4.5 8.1 - - + -
586A VAL* 3.5 33.2 - - + -
631A TYR* 1.3 80.2 - - - +
633A SER* 1.3 63.3 + - - +
634A LEU* 3.0 18.2 + - + -
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Residues in contact with SER 633 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
409A ASP* 2.8 28.4 + - - -
416A SER* 3.2 13.3 + - - -
417A LYS 4.0 4.4 - - - -
418A PRO* 4.5 2.4 - - - +
499A ALA 4.4 1.4 - - - +
500A PRO* 3.4 7.4 - - - +
501A ASP* 2.8 45.0 + - - -
503A HIS* 4.3 12.3 - - - -
631A TYR* 3.8 11.5 - - - -
632A ILE* 1.3 69.6 - - - +
634A LEU* 1.3 59.1 + - - +
635A PRO* 3.8 0.7 - - - +
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Residues in contact with LEU 634 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
416A SER* 3.2 2.7 - - - -
417A LYS 2.9 41.1 + - - +
419A LEU* 4.3 17.0 - - + -
429A PHE* 3.9 19.3 - - + -
494A LEU* 4.3 8.7 - - + -
496A ILE* 3.8 28.3 - - + -
500A PRO* 4.6 0.4 - - + -
519A LEU* 3.8 34.3 - - + -
578A PHE* 5.3 2.7 - - + -
584A VAL* 5.5 1.3 - - + -
632A ILE* 3.0 22.6 + - + +
633A SER* 1.3 72.5 + - - +
635A PRO* 1.3 66.3 - - + +
636A VAL* 2.9 21.3 + - + +
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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