Contacts of the strand formed by residues 436 - 440 (chain D) in PDB entry 5MKE
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 PHE 436 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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249D TYR* 5.3 0.4 - - - -
316D LEU* 3.2 39.3 - - + -
427D SER* 2.9 28.5 - - - -
428D VAL 3.3 3.1 - - - -
429D TYR* 3.6 12.6 - + + -
435D LEU* 1.3 76.1 - - - +
437D CYS* 1.3 69.3 + - - +
438D VAL* 4.7 0.9 - - + -
459D PRO 3.1 0.7 - - - -
460D LEU* 2.1 92.7 + - + +
462D LEU* 3.3 33.4 - - + +
536D LEU* 6.2 3.1 - - + -
540D GLU* 6.4 0.4 - - - -
548D PHE* 4.2 20.4 - + + -
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Residues in contact with CYS 437 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249D TYR* 4.4 21.1 - - + +
250D THR* 6.2 5.6 - - - -
253D MET* 5.4 5.6 - - - -
427D SER* 2.1 23.7 + - - -
428D VAL* 2.4 50.1 + - + +
436D PHE* 1.3 76.1 - - - +
438D VAL* 1.3 67.0 - - - +
439D VAL* 5.3 2.2 - - - -
457D PHE* 5.1 8.7 - - - -
458D GLN 3.0 30.7 - - - -
459D PRO* 3.8 7.0 - - + -
460D LEU 4.1 0.7 - - - +
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Residues in contact with VAL 438 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
426D PHE 4.4 1.1 - - - +
427D SER* 3.1 22.4 - - - +
436D PHE* 4.7 3.4 - - + -
437D CYS* 1.3 78.0 - - - +
439D VAL* 1.3 63.4 + - - +
440D ARG* 5.3 6.5 - - + +
456D GLN* 3.8 3.1 - - + +
457D PHE* 3.4 21.3 - - - -
458D GLN* 2.7 48.1 + - + +
460D LEU* 5.3 3.4 - - + -
548D PHE* 4.6 5.8 - - + -
549D GLU* 5.8 2.2 - - - -
552D ALA* 3.6 30.5 - - + -
556D ILE* 5.0 5.4 - - + -
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Residues in contact with VAL 439 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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257D PHE* 6.3 4.0 - - + -
287D LEU* 5.3 2.2 - - + -
425D ASP* 3.2 3.6 - - - +
426D PHE* 2.5 91.3 + - + +
428D VAL* 4.6 12.8 - - + -
437D CYS* 5.3 2.9 - - - -
438D VAL* 1.3 78.3 - - - +
440D ARG* 1.3 59.9 + - - +
441D LEU* 4.1 20.0 - - + -
456D GLN 4.0 1.6 - - - -
457D PHE* 4.0 20.6 - - + -
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Residues in contact with ARG 440 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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378D SER 3.0 29.3 + - - -
379D HIS* 3.0 31.5 + - + +
423D PHE* 5.9 1.1 - - + -
425D ASP* 3.1 22.7 + - + +
438D VAL* 3.9 6.0 - - + -
439D VAL* 1.3 74.9 - - - +
441D LEU* 1.3 59.4 + - - +
442D LEU* 5.5 0.2 - - - +
455D TRP 3.4 0.2 - - - -
456D GLN* 2.5 70.0 + - + +
549D GLU* 3.6 34.2 + - + +
553D TYR* 4.4 11.9 - - - +
556D ILE* 4.8 9.8 - - - +
1007D PX6 2.9 28.7 + - - -
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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