Contacts of the strand formed by residues 389 - 396 (chain A) in PDB entry 4F1Z
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 389 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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272A ASP* 5.3 2.4 + - - -
275A ASN* 3.2 22.8 + - - +
381A VAL* 3.7 0.5 - - - -
382A ASP* 2.8 36.5 + - - +
387A GLN* 3.9 20.0 - - + +
388A ASN* 1.3 77.8 - - - +
390A TYR* 1.3 65.6 + - - +
391A LYS* 5.1 13.6 + - - +
490A GLU* 6.5 0.2 - - - -
491A GLY 3.3 5.8 - - - +
492A HIS* 3.0 35.2 - - + +
493A TYR* 3.9 3.5 - - - -
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Residues in contact with TYR 390 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378A ILE* 4.4 8.1 - - + -
380A GLY 3.1 10.5 - - - +
381A VAL* 4.3 7.0 - - + -
389A THR* 1.3 75.5 - - - +
391A LYS* 1.3 68.9 + - - +
392A GLN* 4.2 23.8 + - + -
410A ILE* 5.4 2.1 - - - +
411A LYS 5.1 0.9 + - - -
412A GLY* 5.0 1.7 - - - -
422A GLY* 4.9 1.6 - - - -
424A VAL* 3.7 24.6 - - - +
429A THR* 5.3 0.3 + - - +
489A VAL* 3.5 27.4 - - + +
490A GLU* 3.5 2.9 - - - -
491A GLY* 2.8 46.2 + - - +
492A HIS 3.6 33.4 - - - -
493A TYR* 4.4 1.8 - + + -
500A LEU* 3.7 41.1 - - + -
502A THR* 4.8 12.6 - - + +
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Residues in contact with LYS 391 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272A ASP* 4.2 20.9 - - + +
274A SER* 5.6 1.8 - - - -
275A ASN* 5.9 2.2 - - - +
378A ILE* 3.4 4.3 - - - +
379A ILE* 2.8 42.7 + - + -
380A GLY* 2.6 25.2 + - - +
389A THR* 5.1 13.8 - - - +
390A TYR* 1.3 80.0 + - - +
392A GLN* 1.3 56.6 + - - +
489A VAL 3.4 3.6 - - - +
490A GLU* 2.6 50.9 + - - +
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Residues in contact with GLN 392 (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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376A SER* 3.5 6.9 + - - -
377A GLN 2.9 20.6 - - - +
378A ILE* 3.9 8.7 - - - +
379A ILE* 4.4 1.3 - - - +
390A TYR* 4.2 15.3 + - + -
391A LYS* 1.3 75.8 - - - +
393A THR* 1.3 67.2 + - - +
394A VAL* 4.3 7.3 - - + +
410A ILE* 4.0 15.1 - - - +
487A VAL 3.4 3.6 - - - +
488A LEU* 3.8 2.5 - - - -
489A VAL* 2.9 59.6 + - + +
502A THR* 3.1 21.4 + - - -
504A VAL* 4.3 4.4 - - - +
524A ASN* 2.9 27.1 - - - +
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Residues in contact with THR 393 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
376A SER* 2.9 3.5 - - - -
377A GLN 2.7 38.1 + - - -
379A ILE* 3.1 22.1 - - - +
392A GLN* 1.3 71.5 - - - +
394A VAL* 1.3 58.5 + - - +
395A PHE* 3.3 20.4 - - + -
446A TYR* 2.8 34.1 + - - +
448A ALA* 4.0 10.1 + - + -
486A VAL* 3.7 24.7 - - + -
487A VAL 3.7 2.2 - - - -
488A LEU* 4.1 8.5 - - + +
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Residues in contact with VAL 394 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
374A ILE* 3.6 26.7 - - + -
375A SER 3.4 12.1 - - - +
376A SER* 3.7 12.3 - - - -
392A GLN* 4.3 10.8 - - - +
393A THR* 1.3 75.0 - - - +
395A PHE* 1.3 69.5 + - - +
396A VAL* 4.0 8.7 + - + -
408A VAL* 5.3 0.2 - - + -
410A ILE* 3.6 29.2 - - + -
486A VAL* 3.6 5.5 - - - +
487A VAL* 2.9 45.2 + - + +
489A VAL* 4.4 5.8 - - + -
504A VAL* 4.0 7.0 - - + -
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Residues in contact with PHE 395 (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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362A PRO* 5.2 7.0 - - + -
363A ILE* 6.3 1.8 - - + -
374A ILE* 2.9 23.1 - - - +
375A SER* 2.7 29.7 + - - +
393A THR* 3.3 28.7 - - + -
394A VAL* 1.3 78.4 - - - +
396A VAL* 1.3 62.1 + - - +
398A PRO* 3.5 15.2 - - + +
442A LEU* 3.8 40.8 - - + -
443A SER* 4.2 13.5 - - - -
446A TYR* 3.5 46.9 - + - -
447A TYR 4.6 2.2 - - - -
448A ALA* 5.1 1.3 - - + -
484A THR* 4.9 4.7 - - + -
485A TYR 3.7 4.0 - - - +
486A VAL* 4.5 12.8 - - + -
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Residues in contact with VAL 396 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
374A ILE* 4.2 4.5 - - + -
394A VAL* 4.0 16.4 - - + -
395A PHE* 1.3 74.5 - - - +
397A ASN* 1.3 73.6 + - + +
398A PRO* 3.3 0.9 - - - -
406A THR* 4.9 1.1 - - + -
408A VAL* 3.9 27.1 - - + -
478A PHE* 4.0 34.5 - - + -
481A ILE* 4.6 8.3 - - + -
484A THR* 3.3 1.2 - - - +
485A TYR* 2.9 40.5 + - + +
487A VAL* 4.3 8.7 - - + -
506A GLN* 3.7 15.9 - - - +
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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