Contacts of the strand formed by residues 381 - 385 (chain E) in PDB entry 4R2G
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 GLU 381 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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298E ARG* 2.6 33.8 + - - -
377E ASN* 3.4 7.2 + - - -
378E CYS 3.1 30.9 + - - +
379E GLY 3.1 1.6 - - - +
380E GLY* 1.3 78.6 - - - +
382E PHE* 1.3 62.0 + - - +
383E PHE* 3.4 16.8 + - + -
420E ILE* 3.4 14.9 - - + +
421E LYS 4.8 2.9 - - - +
422E GLN* 5.0 6.8 + - - +
437E PRO* 5.1 1.0 - - - +
438E PRO* 3.6 28.3 - - + +
443E ILE* 3.4 39.8 - - + +
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Residues in contact with PHE 382 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112E TRP* 3.8 22.0 - + - -
116E LEU* 4.9 4.3 - - + -
376E PHE 3.8 6.3 - - - -
377E ASN* 3.6 20.4 - - + -
380E GLY* 4.2 11.9 - - - -
381E GLU* 1.3 72.8 + - - +
383E PHE* 1.3 64.6 + - - +
384E TYR* 3.7 8.4 - - + -
420E ILE* 3.5 4.1 - - - +
421E LYS 3.0 45.2 + - - +
422E GLN* 5.1 0.7 - - + -
424E ILE* 3.5 35.0 - - + -
427E TRP* 6.1 0.2 - + - -
435E TYR* 3.3 56.8 - + + -
436E ALA 5.7 0.7 - - - -
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Residues in contact with PHE 383 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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296E CYS* 4.2 4.5 - - + -
297E THR* 4.0 37.5 - - - -
298E ARG* 4.2 1.3 - - + -
329E ALA* 4.6 2.5 - - + -
375E SER* 3.3 6.2 - - - -
376E PHE* 2.9 70.4 + + + +
378E CYS* 3.5 23.1 - - + -
381E GLU* 3.5 31.2 - - + -
382E PHE* 1.3 72.2 - - - +
384E TYR* 1.3 64.0 + - - +
385E CYS* 4.1 12.1 - - - -
418E CYS* 4.2 6.7 - - + -
419E ARG 3.8 3.4 - - - -
420E ILE* 3.5 27.4 - - + -
443E ILE* 4.2 10.1 - - + -
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Residues in contact with TYR 384 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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369E PRO* 3.7 25.6 - - + -
370E GLU* 2.4 54.3 + - + +
373E MET* 3.8 21.5 - - + +
374E HIS 4.0 2.2 - - - -
375E SER* 4.1 9.2 - - - +
382E PHE* 3.7 14.8 - + + -
383E PHE* 1.3 75.9 - - - +
385E CYS* 1.3 60.6 + - - +
417E PRO 4.2 0.2 - - - +
418E CYS* 3.1 2.8 - - - -
419E ARG* 2.7 46.4 + - + +
421E LYS* 3.4 44.0 - - + +
424E ILE* 3.3 25.8 - - + +
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Residues in contact with CYS 385 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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331E CYS* 3.2 21.1 - - - -
373E MET* 3.4 9.2 - - - +
374E HIS* 2.9 47.1 + - + +
376E PHE* 3.4 20.0 - - + -
383E PHE* 4.1 3.1 - - - -
384E TYR* 1.3 75.3 - - - +
386E ASN* 1.3 61.8 + - - +
387E SER 3.5 0.5 + - - -
416E LEU* 4.7 7.0 - - + -
417E PRO 3.5 3.8 - - - -
418E CYS* 2.1 44.4 - - - -
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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