Contacts of the strand formed by residues 448 - 456 (chain A) 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 VAL 448 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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434A ILE* 4.1 19.1 - - + -
437A PHE* 4.6 9.0 - - + -
438A ARG* 3.6 42.4 - - + +
441A TRP* 4.0 12.8 - - + -
446A GLN 3.5 11.0 + - - +
447A PRO* 1.3 75.2 - - - +
449A GLN* 1.3 61.8 + - - +
450A VAL* 4.0 22.2 - - + -
468A PHE 3.7 1.6 - - - +
469A THR* 3.3 4.6 - - - -
470A TYR* 2.9 39.6 + - + +
235C ASN* 5.5 1.8 - - - -
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Residues in contact with GLN 449 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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447A PRO 4.3 0.8 + - - -
448A VAL* 1.3 73.8 - - - +
450A VAL* 1.3 64.0 + - - +
451A PRO* 4.6 1.2 - - - +
467A THR* 2.6 34.4 + - + +
468A PHE 3.5 2.2 - - - -
469A THR* 3.5 25.6 + - + +
235C ASN* 5.6 2.8 + - - -
330C ARG* 5.9 1.4 + - - -
194D MET* 3.4 49.7 - - + +
195D LYS 3.4 17.6 + - - +
197D ASN* 5.0 0.8 + - - +
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Residues in contact with VAL 450 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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412A PHE* 4.2 7.6 - - + -
413A GLY* 4.2 9.2 - - - +
437A PHE* 3.7 34.8 - - + -
448A VAL* 4.0 14.8 - - + -
449A GLN* 1.3 79.4 - - - +
451A PRO* 1.4 70.4 - - + +
467A THR* 3.2 5.0 - - - -
468A PHE* 2.7 57.9 + - + +
470A TYR* 3.8 24.2 - - + -
194D MET* 5.2 0.2 - - - -
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Residues in contact with PRO 451 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66A LEU* 3.9 27.8 - - + -
69A ARG* 4.3 20.9 - - - +
411A TRP 3.3 1.4 - - - +
412A PHE* 3.3 5.7 - - - -
413A GLY* 2.9 37.0 + - - -
449A GLN 4.6 2.2 - - - +
450A VAL* 1.4 87.2 - - + +
452A VAL* 1.3 61.5 + - - +
453A THR* 4.0 7.5 + - + +
466A LEU 3.9 8.3 - - - +
467A THR* 4.1 9.1 - - + -
194D MET* 4.8 6.7 - - + -
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Residues in contact with VAL 452 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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386A LEU* 4.2 29.6 - - + -
397A LEU* 4.3 9.9 - - + -
399A LEU* 4.4 7.2 - - + -
410A VAL* 3.7 25.6 - - + -
411A TRP 3.4 2.7 - - - -
412A PHE* 4.4 7.2 - - + -
451A PRO* 1.3 74.1 - - - +
453A THR* 1.3 63.1 + - - +
463A SER* 5.5 0.2 - - - -
464A THR* 2.9 35.7 + - + +
466A LEU 3.1 13.1 + - - +
467A THR 3.9 4.3 - - - -
468A PHE* 3.8 33.7 - - + +
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Residues in contact with THR 453 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62A MET* 4.5 7.9 - - + +
65A TYR* 4.6 6.5 - - + -
66A LEU* 5.1 2.0 - - + +
410A VAL* 3.6 3.5 - - - +
411A TRP* 2.8 48.2 + - - +
413A GLY 4.3 6.4 + - - -
451A PRO* 4.1 12.9 + - + +
452A VAL* 1.3 76.2 - - - +
454A LEU* 1.3 61.6 + - - +
455A VAL* 4.6 3.6 - - - -
461A ILE* 3.5 32.1 - - + -
462A TYR 3.7 3.6 - - - +
463A SER* 3.7 22.9 - - - -
464A THR* 4.4 1.3 - - - -
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Residues in contact with LEU 454 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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381A PRO* 3.9 22.4 - - + +
383A VAL* 3.7 30.7 - - + -
399A LEU* 4.5 6.5 - - + -
404A PHE* 3.9 16.6 - - + -
408A LEU* 4.4 11.7 - - + -
409A ARG 3.6 7.2 - - - +
410A VAL* 3.7 29.6 - - + -
427A MET* 4.1 17.7 - - - -
453A THR* 1.3 73.4 - - - +
455A VAL* 1.3 62.4 + - - +
462A TYR* 2.9 47.8 + - + +
464A THR* 4.5 4.4 - - + +
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Residues in contact with VAL 455 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57A LEU* 3.7 41.5 - - + -
62A MET* 4.4 6.7 - - - -
408A LEU* 3.3 6.2 - - - -
409A ARG* 2.7 35.3 + - + +
411A TRP* 3.5 40.4 - - + +
453A THR* 4.6 4.7 - - - +
454A LEU* 1.3 79.1 - - - +
456A ARG* 1.4 72.3 + - - +
459A GLY 4.9 0.7 - - - +
460A VAL 3.5 9.2 - - - +
461A ILE* 4.2 10.1 - - + -
462A TYR* 5.2 0.2 - - - -
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Residues in contact with ARG 456 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56A ARG* 5.4 0.7 - - - -
57A LEU 4.8 3.3 + - - -
375A ALA* 3.7 11.5 + - - +
376A PRO 2.7 33.9 + - - -
377A VAL* 3.8 5.1 + - - +
378A THR 4.4 5.1 + - - -
379A PRO* 5.3 3.2 + - - +
405A THR* 5.5 0.7 - - - -
407A ASN* 3.7 27.8 - - - +
408A LEU* 4.2 10.5 - - + +
409A ARG* 6.1 1.1 - - - -
455A VAL* 1.4 83.1 - - - +
457A ASN* 1.3 77.2 + - - +
458A ASP* 2.8 39.4 + - - +
459A GLY* 3.1 11.8 + - - -
460A VAL* 2.8 30.8 + - - +
462A TYR* 3.2 30.2 + - + -
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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