Contacts of the strand formed by residues 452 - 456 (chain m) in PDB entry 6QX2
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 GLN 452 (chain m).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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421m CYS* 3.5 5.1 - - - +
430m GLU* 3.0 31.5 + - + +
432m PHE* 3.6 22.0 - - + -
447m ARG* 2.8 52.4 + - + +
448m ASP* 2.8 41.0 + - - +
451m THR* 1.3 85.7 - - - +
453m ALA* 1.3 52.5 - - - +
592m TRP* 3.4 10.0 - - - -
596m MET* 2.8 31.2 + - - +
598m PRO* 4.7 3.0 - - - +
601m ARG* 3.5 2.4 - - - +
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Residues in contact with ALA 453 (chain m).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
418m LEU* 4.2 2.5 - - + -
419m ALA 3.3 12.8 - - - +
420m ASP* 3.8 11.7 - - - +
421m CYS* 3.9 4.1 - - - +
430m GLU 2.8 7.9 + - - +
431m ILE* 3.5 6.7 - - + -
432m PHE* 2.9 26.0 + - - -
447m ARG* 3.9 0.7 - - - +
452m GLN* 1.3 72.9 - - - +
454m ILE* 1.3 67.7 + - - +
500m TYR* 3.5 38.8 - - + +
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Residues in contact with ILE 454 (chain m).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
418m LEU* 3.4 5.5 - - - +
419m ALA* 2.8 38.4 + - - +
431m ILE* 4.7 0.7 - - - -
432m PHE* 3.4 10.1 - - + +
434m VAL* 4.0 24.0 - - + -
440m GLY* 4.3 13.5 - - - +
443m THR* 3.4 32.1 - - + +
444m LYS* 3.5 31.4 - - + +
447m ARG* 3.5 32.3 - - + +
453m ALA* 1.3 78.9 - - - +
455m LEU* 1.3 61.1 + - - +
456m PRO* 3.7 10.2 - - + +
596m MET* 4.9 1.3 - - + -
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Residues in contact with LEU 455 (chain m).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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418m LEU* 4.2 24.5 - - + +
431m ILE* 4.0 11.5 - - + +
432m PHE 2.9 8.2 + - - -
433m LEU* 3.5 23.3 - - + +
434m VAL* 3.4 19.3 + - - -
454m ILE* 1.3 72.1 - - - +
456m PRO* 1.4 70.7 - - + +
457m LEU* 3.5 9.9 + - + +
480m GLN* 3.7 33.7 - - + +
481m MET* 3.7 42.6 - - + +
484m ALA* 4.2 9.4 - - + -
485m PHE* 5.6 0.4 - - + -
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Residues in contact with PRO 456 (chain m).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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417m LYS* 2.9 43.0 - - + +
434m VAL* 3.6 15.2 - - + +
436m GLY 3.7 22.2 - - - +
437m ASP* 3.9 19.6 - - - +
440m GLY* 4.3 11.4 - - - -
444m LYS* 5.6 5.2 - - + -
454m ILE* 3.7 7.4 - - + +
455m LEU* 1.4 89.6 - - + +
457m LEU* 1.3 63.1 + - - +
458m ARG* 5.1 2.1 - - - +
477m GLU* 5.0 2.6 - - - +
480m GLN* 4.9 1.4 - - - +
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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