Contacts of the strand formed by residues 388 - 393 (chain C) in PDB entry 1JXQ
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 GLY 388 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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330C SER* 3.9 1.4 + - - -
331C TYR* 2.6 41.9 + - - +
374C ALA* 5.7 1.1 - - - -
387C PRO* 1.3 76.0 - - - +
389C CYS* 1.3 59.3 + - - +
392D ASN 3.2 13.9 - - - -
393D PHE* 3.2 20.4 - - - -
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Residues in contact with CYS 389 (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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328C PHE* 3.2 33.0 - - + -
329C VAL 2.9 20.4 - - - +
330C SER* 3.4 11.9 - - - -
331C TYR* 4.2 2.7 - - - +
367C GLN* 3.8 21.8 - - - -
370C LEU* 4.8 9.6 - - - -
388C GLY* 1.3 77.3 - - - +
390C PHE* 1.3 64.2 + - - +
392C ASN 3.5 1.3 + - - -
389D CYS 3.3 2.4 - - - +
390D PHE* 3.8 0.5 - - - -
392D ASN* 2.9 37.9 + - - +
393D PHE* 4.2 1.6 - - - -
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Residues in contact with PHE 390 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240C PHE* 3.6 67.9 + - + +
327C ILE 3.9 0.7 - - - +
328C PHE* 3.5 4.2 + - - -
329C VAL* 2.9 34.4 + - + +
331C TYR* 3.1 32.8 - + + -
335C PRO* 4.7 0.2 - - + -
389C CYS* 1.3 74.3 - - - +
392C ASN* 1.3 59.9 + - - +
393C PHE* 3.7 7.9 + + + -
240D PHE* 3.8 26.2 - - + -
389D CYS 3.6 3.6 - - - -
390D PHE* 3.2 44.9 - + + -
393D PHE* 3.9 21.1 - + - -
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Residues in contact with ASN 392 (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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328C PHE* 3.3 26.1 - - + -
367C GLN* 2.9 33.2 + - - +
389C CYS 3.5 2.9 + - - +
390C PHE* 1.3 70.0 - - - +
393C PHE* 1.3 61.1 + - - +
394C LEU* 2.8 33.7 + - - +
371D LEU* 4.3 11.4 - - - +
387D PRO 4.6 0.3 - - - +
388D GLY* 3.7 2.3 - - - -
389D CYS* 2.9 47.0 + - + +
392D ASN* 5.4 1.6 - - + -
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Residues in contact with PHE 393 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240C PHE* 3.4 74.7 - - + -
324C PRO* 3.8 22.0 - - + -
326C ASP 3.1 8.5 + - - -
327C ILE* 2.8 29.7 + - + +
390C PHE* 4.3 6.3 - - + -
392C ASN* 1.3 75.9 - - - +
394C LEU* 1.3 61.0 + - - +
386D MET* 3.1 44.2 - - + +
387D PRO 3.3 19.3 - - - -
388D GLY* 3.4 23.8 - - - -
389D CYS 5.2 0.2 - - - -
390D PHE* 4.5 8.7 - + - -
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Residues in contact with LEU 394 (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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153C TYR* 3.5 25.4 - - + +
277C PRO* 3.9 12.1 - - + -
279C LEU* 4.7 1.6 - - + -
326C ASP* 3.8 21.5 - - - +
328C PHE* 3.9 37.2 - - + -
366C LEU* 4.5 14.1 - - + -
367C GLN* 6.1 2.0 - - + +
392C ASN* 2.8 18.5 + - - +
393C PHE* 1.3 81.2 - - - +
395C ARG* 1.3 59.3 + - - +
396C LYS 3.8 18.8 - - - +
398C LEU* 4.8 8.3 - - + +
371D LEU* 3.6 14.0 - - + +
374D ALA* 3.7 14.6 - - - +
386D MET* 4.4 0.3 - - - +
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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