Contacts of the strand formed by residues 414 - 423 (chain D) in PDB entry 4JF7
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 414 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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324D PHE* 5.3 0.4 - - - -
326D PRO* 4.3 11.7 - - + -
386D LEU* 4.0 20.6 - - + -
402D TYR 3.8 0.5 - - - +
403D TYR* 3.4 10.3 - - - -
404D GLN* 3.0 46.7 + - + +
406D SER* 3.7 11.0 + - - +
410D TRP* 3.2 36.1 - - + +
412D MET* 3.3 13.7 + - + +
413D THR* 1.3 93.6 - - - +
415D LEU* 1.3 60.4 + - - +
416D TYR* 4.0 21.5 - - + +
434D ASN* 4.0 22.7 - - - +
435D VAL 5.2 0.2 - - - +
437D THR* 4.7 9.6 - - + +
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Residues in contact with LEU 415 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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394D TYR* 4.9 3.6 - - + -
401D TYR* 5.1 3.4 - - + -
402D TYR 3.4 3.4 - - - +
403D TYR* 3.7 29.6 - - + +
413D THR* 3.9 14.9 + - + +
414D MET* 1.3 80.4 - - - +
416D TYR* 1.3 62.5 + - - +
434D ASN* 2.9 9.1 + - - +
435D VAL* 2.9 42.8 + - + +
466D ALA* 3.8 32.8 - - + +
468D LEU* 4.0 35.4 - - + -
484D PHE* 4.5 12.1 - - + -
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Residues in contact with TYR 416 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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324D PHE* 4.3 3.6 - + - -
384D GLN 3.2 24.0 - - - -
385D VAL* 3.4 14.0 - - + -
386D LEU* 3.6 12.1 + - - +
401D TYR* 3.1 12.6 - - - -
402D TYR* 3.0 55.4 + + + +
404D GLN* 2.8 39.6 + - + -
414D MET* 4.0 21.7 - - + +
415D LEU* 1.3 74.6 - - - +
417D LYS* 1.3 61.9 + - - +
418D VAL* 3.5 0.8 + - + -
432D ALA* 4.0 22.2 - - + -
433D GLN 3.2 7.0 - - - +
434D ASN* 3.6 37.9 - - + -
435D VAL 4.6 0.2 - - - +
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Residues in contact with LYS 417 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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399D SER* 3.3 28.5 + - - +
400D VAL 3.9 3.4 - - - +
401D TYR* 3.6 37.9 - - + +
416D TYR* 1.3 72.7 - - - +
418D VAL* 1.3 67.1 + - - +
419D THR* 3.8 11.8 + - - +
431D SER 3.5 3.8 - - - +
432D ALA* 3.5 0.3 - - - -
433D GLN* 2.9 41.7 + - + +
473D SER* 4.2 12.6 + - - +
478D PHE* 3.8 18.8 - - + -
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Residues in contact with VAL 418 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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362D ILE* 4.2 14.1 - - + -
380D PHE* 4.1 23.8 - - + -
400D VAL* 2.8 40.6 + - + +
401D TYR 4.1 2.2 - - - -
402D TYR* 3.5 37.7 - - + +
416D TYR* 3.9 4.3 - - + +
417D LYS* 1.3 79.4 - - - +
419D THR* 1.3 61.4 + - - +
420D ILE* 3.9 20.3 + - + +
430D ILE* 4.2 8.1 - - + -
431D SER 3.2 9.6 - - - +
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Residues in contact with THR 419 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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417D LYS* 3.8 13.6 + - - +
418D VAL* 1.3 71.6 - - - +
420D ILE* 1.3 68.5 + - - +
421D THR* 4.0 12.2 + - + +
429D ALA 4.0 0.3 - - - +
430D ILE* 3.5 2.9 - - - -
431D SER* 2.8 51.4 + - - -
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Residues in contact with ILE 420 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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297D TYR* 4.1 15.0 + - + +
302D LEU* 3.6 33.2 - - + -
362D ILE* 5.3 3.1 - - + -
378D LEU* 5.5 0.4 - - + -
400D VAL* 4.1 21.1 - - + -
418D VAL* 3.9 17.9 + - + +
419D THR* 1.3 80.5 - - - +
421D THR* 1.3 71.8 + - - +
422D PHE* 3.8 29.4 - - + -
427D PRO* 4.1 16.6 - - + -
429D ALA 3.6 8.1 - - - +
430D ILE* 4.1 10.5 - - + -
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Residues in contact with THR 421 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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419D THR* 4.8 13.9 - - + +
420D ILE* 1.3 76.1 - - - +
422D PHE* 1.3 59.2 + - - +
423D THR* 5.8 0.2 - - - -
427D PRO* 3.3 4.3 - - - +
428D SER* 2.7 37.9 + - - -
429D ALA* 3.0 33.1 + - + +
431D SER* 6.5 0.4 - - - -
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Residues in contact with PHE 422 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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297D TYR* 4.1 28.5 - + - -
298D LEU* 4.3 20.4 - - + -
300D TRP* 4.2 18.4 - + + -
302D LEU* 6.4 0.9 - - + -
420D ILE* 3.8 24.2 - - + -
421D THR* 1.3 79.0 - - - +
423D THR* 1.3 61.6 + - - +
424D ASN 4.1 1.1 + - - -
425D GLY* 3.9 16.2 - - - +
426D GLN 3.2 9.2 - - - +
427D PRO* 3.5 37.5 - - + -
428D SER* 3.8 0.2 - - - -
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Residues in contact with THR 423 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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421D THR* 5.8 0.2 - - - -
422D PHE* 1.3 72.4 + - - +
424D ASN* 1.3 86.9 + - + +
425D GLY 3.2 0.7 - - - -
426D GLN* 2.7 24.6 + - - +
428D SER* 2.9 28.6 + - - -
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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