Contacts of the strand formed by residues 334 - 339 (chain C) in PDB entry 1JLH
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 THR 334 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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327C ILE* 5.8 1.0 - - - +
332C CYS* 3.4 4.3 - - - +
333C GLU* 1.3 89.2 - - + +
335C HIS* 1.3 62.6 + - - +
376C PRO* 4.3 3.5 - - - +
377C ILE* 3.1 20.6 - - + +
379C TRP* 3.1 20.1 + - + +
400C MET 5.2 0.7 + - - -
401C ILE* 3.9 10.2 - - - +
402C PRO* 3.4 25.0 - - - +
333D GLU* 4.2 3.4 + - - +
334D THR* 3.5 31.6 - - + -
377D ILE* 3.5 19.9 - - + +
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Residues in contact with HIS 335 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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323C GLY* 6.0 3.7 - - - -
327C ILE* 6.2 0.2 - - + -
334C THR* 1.3 74.7 - - - +
336C ALA* 1.3 62.4 + - - +
337C MET* 3.7 25.6 + - + +
355C ASP* 5.4 2.5 - - - -
376C PRO* 4.2 20.2 - - + -
377C ILE 2.9 7.0 + - - +
378C VAL* 3.4 12.4 - - + +
379C TRP* 3.2 24.5 + - - +
402C PRO* 3.7 23.1 + - + +
404C ASP* 2.8 42.9 + - - -
474C ASN* 5.1 3.1 - - - -
493C TYR* 4.7 0.2 - - - -
496C LYS* 3.4 26.2 + - - -
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Residues in contact with ALA 336 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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335C HIS* 1.3 75.2 + - - +
337C MET* 1.3 62.6 + - - +
338C LEU* 4.0 13.9 - - + -
379C TRP* 3.4 34.9 - - + +
394C ILE* 5.3 0.2 - - + -
401C ILE* 4.1 2.2 - - + +
402C PRO 3.0 13.9 + - - +
403C CYS* 3.4 19.4 - - - -
404C ASP* 2.9 27.0 + - - +
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Residues in contact with MET 337 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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335C HIS* 3.7 23.1 - - + +
336C ALA* 1.3 75.8 - - - +
338C LEU* 1.3 68.3 + - - +
339C PRO* 3.4 11.5 - - + +
347C PHE* 3.7 25.4 - - + +
348C ALA* 3.7 23.7 - - + +
351C PHE* 3.9 22.9 - - + -
355C ASP* 5.9 1.6 - - - +
378C VAL* 3.9 24.2 - - + -
379C TRP 2.9 11.2 + - - +
380C GLY* 3.7 4.5 - - - -
404C ASP* 3.8 7.9 - - + +
406C LEU* 4.9 3.8 - - + -
493C TYR* 3.5 40.8 - - + +
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Residues in contact with LEU 338 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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336C ALA* 4.3 6.5 - - + -
337C MET* 1.3 81.7 - - - +
339C PRO* 1.3 64.1 - - - +
340C TYR* 3.5 10.7 + - + -
380C GLY* 3.9 4.9 - - - -
381C GLU 3.5 28.7 - - - +
383C GLY 5.0 0.2 - - - -
390C PHE* 3.9 18.4 - - + -
391C TYR* 3.4 32.1 - - + +
394C ILE* 4.6 4.9 - - + -
403C CYS* 4.1 17.9 - - + -
404C ASP 2.8 16.4 + - - +
405C PHE* 3.5 27.7 - - + -
406C LEU* 3.3 17.6 + - - +
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Residues in contact with PRO 339 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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337C MET* 3.4 12.1 - - + +
338C LEU* 1.3 83.9 - - - +
340C TYR* 1.3 51.6 + - - +
341C ASP* 2.9 7.6 + - + -
344C LEU* 3.6 50.3 - - + +
347C PHE* 4.3 13.9 - - + -
348C ALA* 5.2 4.3 - - + +
381C GLU 4.2 0.7 - - - +
382C PRO* 3.0 15.1 - - + +
383C GLY 2.6 27.1 + - - -
406C LEU* 3.5 23.3 - - + +
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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