Contacts of the strand formed by residues 396 - 402 (chain C) in PDB entry 4J2X
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 MET 396 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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388C LEU* 3.3 5.2 - - - -
389C ASN* 2.8 46.1 + - + +
390C GLY* 3.5 6.9 + - - +
394C VAL* 4.0 14.6 + - + +
395C ALA* 1.3 75.8 - - - +
397C LEU* 1.3 59.8 + - - +
398C GLU 4.0 0.2 + - - -
428C LEU* 3.7 29.2 - - + -
429C CYS* 3.5 22.0 - - - +
430C VAL* 4.0 22.0 - - + -
431C VAL* 4.3 1.8 - - - -
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Residues in contact with LEU 397 (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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386C LEU* 3.7 37.9 - - + -
387C GLN* 3.6 24.2 - - - +
388C LEU* 4.2 6.3 - - + +
396C MET* 1.3 72.5 - - - +
398C GLU* 1.4 62.0 + - - +
399C LEU* 4.0 1.8 - - + +
412C PHE* 3.7 25.8 - - + -
427C MET 3.8 0.9 - - - +
428C LEU* 3.6 3.4 - - - -
429C CYS* 3.0 47.9 + - - -
431C VAL* 3.8 9.3 - - + +
452C VAL* 4.5 7.4 - - + -
468C PHE* 4.0 26.9 - - + -
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Residues in contact with GLU 398 (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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385C SER 3.9 0.5 - - - +
386C LEU* 3.3 8.1 - - - -
387C GLN* 2.8 46.9 + - + +
388C LEU 4.2 5.7 - - - +
389C ASN* 3.0 44.5 + - - +
397C LEU* 1.4 71.2 - - - +
399C LEU* 1.3 62.6 + - - +
400C THR* 4.0 8.3 + - + +
422C ARG* 3.6 20.7 + - - +
426C SER* 6.3 1.8 - - - -
427C MET 3.6 5.2 - - - +
428C LEU* 3.9 12.8 - - + -
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Residues in contact with LEU 399 (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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383C VAL* 4.2 17.9 - - + -
385C SER 3.8 4.7 - - - -
386C LEU* 3.5 23.6 - - + -
397C LEU* 4.0 12.1 - - + +
398C GLU* 1.3 70.4 - - - +
400C THR* 1.3 61.5 + - - +
404C PHE* 3.3 13.5 - - + -
410C VAL* 3.6 29.6 - - + -
426C SER* 3.3 3.3 - - - -
427C MET* 2.7 61.3 + - + +
429C CYS* 4.1 8.5 - - + -
452C VAL* 4.4 4.9 - - + -
454C LEU* 3.9 26.7 - - + -
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Residues in contact with THR 400 (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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383C VAL* 3.7 2.4 - - - +
384C GLU* 2.7 41.5 + - - +
385C SER* 3.0 33.2 + - - -
398C GLU* 4.0 8.6 + - + +
399C LEU* 1.3 77.3 - - - +
401C GLY* 1.3 52.1 + - - +
404C PHE* 3.9 2.5 - - - -
425C GLU 3.3 7.9 - - - +
426C SER* 4.5 11.2 - - - -
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Residues in contact with GLY 401 (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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382C VAL 3.0 14.8 - - - -
384C GLU* 3.6 19.6 + - - +
400C THR* 1.3 74.3 - - - +
402C GLN* 1.4 67.4 + - - +
404C PHE* 3.5 5.1 - - - -
424C GLY 4.0 0.9 - - - -
425C GLU* 2.8 35.8 + - - +
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Residues in contact with GLN 402 (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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185C LYS* 5.0 10.3 + - - +
364C TYR* 5.5 2.4 + - - -
381C PRO* 3.3 1.7 - - - +
382C VAL* 2.9 42.1 + - + +
384C GLU* 3.2 20.0 + - - +
401C GLY* 1.4 76.9 - - - +
403C ASN* 1.4 81.8 + - - +
404C PHE* 3.3 9.5 + - - -
424C GLY 3.4 6.9 + - - -
425C GLU* 4.8 8.3 - - + +
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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