Contacts of the strand formed by residues 434 - 440 (chain x) in PDB entry 5GJQ
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 HIS 434 (chain x).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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108x ASN* 5.9 0.4 - - - -
113x CYS* 3.8 13.6 - - + -
424x THR 3.4 8.5 - - - +
425x HIS* 4.5 0.6 + - - -
426x GLN* 3.3 25.2 + - + +
433x GLY* 1.3 74.1 - - - +
435x TYR* 1.3 64.3 + - - +
436x VAL* 3.5 24.5 - - + +
450x ASP* 3.2 29.2 + - - -
451x ASP* 3.4 28.3 - - - -
472x HIS* 3.6 16.3 - + - -
75y GLY* 4.5 1.2 - - - -
76y GLZ 3.6 12.7 - - - -
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Residues in contact with TYR 435 (chain x).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113x CYS* 3.0 32.5 - - - +
114x TYR* 3.1 25.6 - - + -
117x ALA* 3.9 13.4 - - + +
198x ASP* 3.4 8.9 + - - -
199x ALA* 2.8 51.4 + - + +
423x LEU* 4.2 10.3 - - + -
424x THR 3.2 2.9 - - - +
425x HIS* 3.0 39.7 - + + -
434x HIS* 1.3 75.3 + - - +
436x VAL* 1.3 65.1 + - - +
449x PHE 5.4 0.3 - - - +
450x ASP* 5.5 0.2 - - - +
451x ASP* 4.9 1.9 + - - +
475x TYR* 4.5 4.9 - + - -
73y LEU* 2.2 36.9 + - + +
75y GLY* 3.5 11.9 - - - -
76y GLZ 3.6 0.2 + - - -
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Residues in contact with VAL 436 (chain x).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117x ALA* 4.4 3.8 - - - -
424x THR 2.8 29.6 + - - +
434x HIS* 3.5 18.8 - - + +
435x TYR* 1.3 82.5 - - - +
437x SER* 1.3 71.9 + - - +
438x TRP* 2.9 33.4 + - + +
448x LYS* 3.9 16.8 - - + -
449x PHE 3.8 14.6 - - - +
450x ASP* 4.1 9.6 - - + +
472x HIS* 3.3 28.9 - - + +
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Residues in contact with SER 437 (chain x).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117x ALA* 3.6 33.6 + - - +
120x GLN* 3.8 12.9 - - - +
121x CYS* 3.4 25.4 + - - -
422x VAL 3.8 6.3 - - - -
423x LEU* 4.6 0.2 - - - +
436x VAL* 1.3 75.6 - - - +
438x TRP* 1.3 70.0 + - - +
439x VAL* 4.2 5.6 - - - +
449x PHE* 3.2 34.7 + - - +
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Residues in contact with TRP 438 (chain x).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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421x ALA* 3.6 1.0 - - - -
422x VAL* 3.0 40.9 + - + -
424x THR* 2.7 24.9 + - - -
436x VAL* 2.9 31.1 + - + -
437x SER* 1.3 81.4 + - - +
439x VAL* 1.3 61.7 + - - +
446x TRP* 3.6 20.1 + - + +
447x ILE 3.2 10.5 - - - +
448x LYS* 3.5 40.8 - - + -
457x VAL* 4.2 14.1 - - + -
461x ASP* 6.0 3.6 - - + -
462x ILE* 4.0 18.6 - - + -
465x LEU* 3.8 23.8 - - + -
471x TRP* 4.6 11.2 - + - -
472x HIS* 3.8 24.0 - + - -
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Residues in contact with VAL 439 (chain x).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120x GLN 3.5 28.0 - - - +
124x SER* 3.5 27.6 - - - -
420x GLN* 3.9 8.3 - - + +
421x ALA* 4.2 8.7 - - + -
437x SER* 4.2 6.7 - - - +
438x TRP* 1.3 76.6 - - - +
440x LYS* 1.3 81.9 + - - +
441x ARG* 3.9 25.6 - - - +
446x TRP* 3.8 3.1 - - - -
447x ILE* 2.9 39.0 + - + +
449x PHE* 5.1 11.8 - - + +
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Residues in contact with LYS 440 (chain x).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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350x LEU* 5.5 4.0 + - - +
418x ASP* 4.2 17.7 + - - +
419x LEU 4.0 11.6 + - - +
420x GLN* 3.3 16.5 + - + +
439x VAL* 1.3 82.4 - - - +
441x ARG* 1.3 73.4 + - - +
442x LYS 4.1 23.6 - - - +
443x GLN* 5.3 2.2 - - - +
444x ASP 5.4 2.0 - - - +
445x GLU 4.2 3.1 - - - +
446x TRP* 3.2 55.9 - - + -
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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