Contacts of the strand formed by residues 402 - 408 (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 402 (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* 3.3 11.8 + - - -
359R LYS* 4.7 0.5 + - - +
360R ALA* 3.8 15.5 + - + +
374R GLY* 3.9 15.7 - - - +
375R GLY 3.1 21.8 + - - +
380R ARG 4.2 7.9 - - - -
381R HIS 4.3 3.6 - - - +
382R ILE* 4.1 13.5 - - + -
398R ALA* 3.9 11.2 - - + -
400R SER 3.7 9.9 - - - +
401R GLN* 1.3 73.6 - - - +
403R CYS* 1.3 61.7 + - - +
404R SER 4.2 5.8 - - - +
405R ILE* 4.0 27.8 - - + -
416R SER* 4.3 8.1 - - - -
417R GLY 3.7 3.6 - - - +
418R HIS* 3.9 11.9 - - + -
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Residues in contact with CYS 403 (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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185R TYR* 4.1 20.4 - - + -
359R LYS* 3.3 25.4 - - + +
360R ALA* 3.6 12.0 + - - -
401R GLN* 3.8 4.5 - - - +
402R VAL* 1.3 74.2 - - - +
404R SER* 1.3 84.8 + - - +
417R GLY 3.2 27.2 + - - -
418R HIS* 4.8 0.7 - - - -
446R VAL* 3.3 34.3 - - - +
447R LEU* 3.4 19.1 - - - +
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Residues in contact with SER 404 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316R ARG* 6.2 2.0 - - - +
359R LYS* 5.9 0.7 - - - -
360R ALA* 3.8 6.3 - - - +
402R VAL* 3.6 2.6 - - - +
403R CYS* 1.3 97.5 - - - +
405R ILE* 1.3 68.3 + - - +
415R ILE 4.6 0.2 - - - -
416R SER* 3.3 5.9 - - - -
417R GLY 3.1 23.7 + - - -
448R SER* 3.4 5.0 - - - -
449R LEU* 3.0 46.2 + - - +
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Residues in contact with ILE 405 (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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316R ARG* 5.5 3.5 + - - +
360R ALA* 3.7 16.9 - - + +
361R VAL 4.5 3.6 - - - +
362R ALA* 3.3 31.6 - - + +
372R ALA* 4.0 14.1 - - + +
373R THR* 3.6 40.2 - - - +
374R GLY 3.7 0.2 - - - +
382R ILE* 4.2 14.4 - - + -
402R VAL* 4.0 13.7 - - + -
404R SER* 1.3 82.5 - - - +
406R LEU* 1.3 81.4 + - - +
407R TRP* 4.9 0.4 - - - +
414R LEU* 4.5 11.4 - - + -
415R ILE 3.3 9.0 - - - +
416R SER* 4.3 8.1 - - - -
449R LEU* 5.3 0.4 - - - -
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Residues in contact with LEU 406 (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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362R ALA* 4.5 2.7 - - - -
405R ILE* 1.3 83.7 - - - +
407R TRP* 1.3 65.8 + - - +
414R LEU* 3.5 4.3 - - - +
415R ILE* 2.9 47.8 + - + +
449R LEU* 4.1 18.6 - - + +
450R THR* 3.6 37.0 - - - +
451R MET* 3.7 39.3 - - + +
458R VAL* 4.5 3.8 - - + -
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Residues in contact with TRP 407 (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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362R ALA* 3.3 32.3 + - + -
363R TRP 3.2 20.9 - - - +
364R CYS* 3.8 27.6 - - + -
365R PRO* 3.6 21.6 - - + +
366R TRP* 3.7 22.7 - + + -
370R VAL* 4.0 17.9 - - + -
372R ALA* 3.7 17.9 - - + +
384R ILE* 4.2 3.6 - - + -
405R ILE* 5.0 0.4 - - + -
406R LEU* 1.3 75.7 - - - +
408R SER* 1.3 58.8 + - - +
409R PRO* 3.8 6.7 - - - +
413R GLU 3.7 3.6 - - - -
414R LEU* 3.7 44.2 - - + -
430R TYR* 3.8 31.0 - + - -
451R MET* 3.5 14.7 - - - +
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Residues in contact with SER 408 (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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366R TRP* 3.8 3.6 - - - -
406R LEU 4.2 0.6 + - - -
407R TRP* 1.3 73.2 - - - +
409R PRO* 1.4 65.0 - - - +
410R HIS* 3.1 21.5 - - - +
411R TYR* 4.0 11.3 - - - -
412R LYS* 3.3 4.9 + - - -
413R GLU* 2.8 46.0 + - - +
414R LEU* 5.7 0.7 - - - -
415R ILE* 5.6 4.5 - - - -
451R MET* 4.1 15.5 - - - +
455R GLY 4.5 5.2 + - - -
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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