Contacts of the strand formed by residues 446 - 451 (chain R) in PDB entry 5G04
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 VAL 446 (chain R).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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185R TYR* 5.3 1.2 - - - -
401R GLN* 3.9 10.4 - - - +
403R CYS* 3.3 28.7 - - - +
417R GLY* 4.4 1.8 - - - -
418R HIS 3.2 29.5 + - - +
423R ASN 3.7 19.3 - - - +
425R LEU* 4.1 7.6 - - + -
442R HIS* 3.8 24.0 - - + -
445R ARG* 1.3 75.9 - - - +
447R LEU* 1.3 63.7 + - - +
448R SER 4.1 2.7 - - - +
449R LEU* 3.8 24.0 - - + -
460R SER* 4.3 6.1 - - - -
461R ALA 3.5 12.6 - - - +
462R ALA* 3.9 1.8 - - + -
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Residues in contact with LEU 447 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181R ILE* 4.4 18.4 - - + -
182R ARG 4.3 13.9 - - - +
183R ASN* 3.9 21.1 - - - +
184R ASP 3.9 26.9 - - - +
185R TYR* 4.4 9.4 - - + +
187R LEU 5.6 0.7 - - - +
189R LEU* 4.8 7.0 - - + -
359R LYS* 2.8 28.9 + - - +
403R CYS* 3.4 16.1 - - - +
404R SER* 4.2 0.5 + - - -
445R ARG* 4.1 9.0 - - - +
446R VAL* 1.3 77.4 - - - +
448R SER* 1.3 63.1 + - - +
461R ALA* 2.7 13.2 + - + +
462R ALA* 3.8 24.0 - - - +
463R ALA* 3.8 11.0 - - + +
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Residues in contact with SER 448 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187R LEU 4.0 1.9 + - - -
188R ASN* 4.1 5.7 + - - -
189R LEU* 3.9 16.8 + - - +
190R VAL* 3.6 28.3 - - - +
359R LYS* 3.7 11.6 + - - +
404R SER* 3.4 10.5 - - - -
446R VAL* 4.0 0.6 - - - +
447R LEU* 1.3 86.4 + - - +
449R LEU* 1.3 65.2 + - - +
459R ALA 4.1 0.2 - - - +
460R SER* 3.5 3.1 - - - -
461R ALA* 2.9 31.0 + - - +
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Residues in contact with LEU 449 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190R VAL* 4.8 3.4 - - - +
404R SER* 3.0 32.3 + - - +
406R LEU* 4.1 20.4 - - + +
415R ILE* 4.0 41.5 - - + +
416R SER* 4.0 0.7 - - - -
417R GLY* 3.8 25.6 - - - +
425R LEU* 4.0 10.5 - - + -
446R VAL* 3.8 19.5 - - + -
448R SER* 1.3 81.6 - - - +
450R THR* 1.3 62.9 + - - +
458R VAL* 5.5 1.3 - - + +
459R ALA 3.4 10.5 - - - +
460R SER* 3.8 11.4 - - - -
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Residues in contact with THR 450 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190R VAL* 4.1 24.9 - - + -
191R ASP* 3.7 7.2 + - - -
192R TRP* 3.1 26.5 + - + +
198R LEU* 3.8 29.6 - - + -
406R LEU* 3.6 10.9 - - - +
449R LEU* 1.3 76.9 - - - +
451R MET* 1.3 60.6 + - - +
458R VAL* 3.5 2.4 - - - -
459R ALA* 2.8 50.9 + - + +
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Residues in contact with MET 451 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192R TRP* 3.2 23.9 - - - +
406R LEU* 3.7 30.8 - - + +
407R TRP 3.5 25.1 - - - +
408R SER* 4.1 19.7 - - - +
409R PRO* 5.5 1.6 - - + -
415R ILE* 4.3 7.9 - - + -
450R THR* 1.3 76.4 + - - +
452R SER* 1.3 73.7 + - - +
455R GLY* 3.8 23.6 - - - +
457R THR 3.4 18.6 - - - +
458R VAL* 3.7 15.7 - - + -
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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