Contacts of the strand formed by residues 408 - 412 (chain H) in PDB entry 3E20
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 ILE 408 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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300H PHE* 3.5 1.8 + - - -
301H GLY 3.1 21.8 + - - -
302H VAL* 3.6 38.6 - - + +
305H THR* 3.2 15.7 + - + +
306H MET* 4.6 10.5 - - + -
317H LEU* 5.1 1.6 - - + -
318H LEU 3.5 11.9 - - - +
319H CYS* 4.9 0.9 - - - -
323H LEU* 3.8 24.7 - - + -
373H LEU* 4.5 15.3 - - + -
377H LEU* 4.1 22.4 - - + -
401H PHE* 3.7 5.5 - - - -
405H PHE 3.5 4.8 + - - +
406H GLY* 3.4 10.5 - - - +
407H GLY* 1.3 81.9 - - - +
409H GLY* 1.3 60.8 + - - +
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Residues in contact with GLY 409 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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287H PHE* 4.6 2.2 - - - -
299H CYS 3.2 1.3 - - - -
300H PHE 2.9 18.2 - - - -
305H THR* 3.4 10.1 - - - -
317H LEU* 3.3 4.0 - - - +
318H LEU* 2.7 42.1 + - - +
401H PHE* 3.5 8.9 - - - -
408H ILE* 1.3 76.1 - - - +
410H ALA* 1.3 57.9 + - - +
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Residues in contact with ALA 410 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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287H PHE* 4.1 5.5 - - - -
298H TYR* 3.1 18.4 - - - +
299H CYS* 2.4 32.5 + - - +
305H THR* 4.2 4.3 - - + -
314H VAL* 3.7 30.5 - - + -
316H THR 3.3 13.9 - - - +
317H LEU* 3.9 12.8 - - + -
318H LEU* 4.4 1.6 - - - +
409H GLY* 1.3 76.6 - - - +
411H VAL* 1.3 63.7 + - - +
412H MET 3.6 0.4 + - - -
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Residues in contact with VAL 411 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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283H LEU* 6.1 0.2 - - + -
286H ARG* 3.7 31.2 - - + +
287H PHE* 3.4 44.4 - - + +
290H GLU* 4.6 13.0 - - + -
297H LYS 4.1 5.6 - - - +
315H GLU* 3.2 25.8 + - + +
316H THR* 3.0 27.2 + - - +
318H LEU* 5.6 2.7 - - + -
410H ALA* 1.3 73.0 - - - +
412H MET* 1.3 66.6 + - - +
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Residues in contact with MET 412 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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296H GLY 4.3 7.0 - - - +
297H LYS* 3.4 29.9 - - - +
298H TYR 3.5 21.1 - - - +
299H CYS* 3.1 27.8 - - - -
308H ALA* 3.2 28.0 - - + -
313H ALA 4.4 11.9 - - - +
314H VAL* 4.2 5.8 - - + +
315H GLU* 4.0 10.2 - - - +
410H ALA 3.6 1.4 + - - +
411H VAL* 1.3 79.2 - - - +
413H ARG* 1.3 61.2 + - - +
414H TYR 3.3 20.6 - - - +
416H LEU* 4.5 16.8 - - + +
418H LEU* 4.1 21.5 - - + -
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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