Contacts of the strand formed by residues 411 - 419 (chain A) in PDB entry 4TZ1
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 SER 411 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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264A ARG* 2.8 29.1 + - - +
376A VAL 2.9 7.1 + - - +
377A LYS* 3.9 9.9 - - - +
378A VAL* 3.0 31.6 + - - +
410A THR* 1.3 75.6 - - - +
412A LEU* 1.3 63.2 + - - +
413A GLN* 3.8 25.7 + - - -
438A THR* 4.7 0.7 - - - -
439A ILE* 3.1 22.0 - - - -
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Residues in contact with LEU 412 (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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368A LEU* 4.9 0.9 - - + -
370A VAL* 5.4 0.4 - - + -
378A VAL* 3.4 38.6 - - + -
394A VAL* 4.1 24.7 - - + -
396A VAL* 4.2 19.1 - - + -
410A THR* 5.4 1.8 - - + -
411A SER* 1.3 73.3 - - - +
413A GLN* 1.3 63.8 + - - +
415A VAL* 3.8 22.9 - - + -
431A ILE* 4.1 20.6 - - + -
438A THR* 5.0 0.6 - - + +
439A ILE 3.0 6.7 + - - +
440A ILE* 3.2 27.7 - - + +
441A ASP 2.9 26.5 + - - +
442A HIS 4.7 1.9 - - - +
443A THR* 5.7 2.5 - - - +
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Residues in contact with GLN 413 (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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179A ARG* 4.0 7.4 - - - +
264A ARG* 2.7 30.6 + - - +
265A GLU 4.1 0.9 - - - +
266A LYS* 3.3 41.2 - - + +
267A PRO* 3.7 10.0 - - - +
377A LYS* 5.3 1.2 - - - +
378A VAL 2.9 11.2 + - - +
379A ALA* 3.1 5.9 - - - +
380A GLY 3.0 18.2 + - - -
411A SER* 3.8 19.8 + - - -
412A LEU* 1.3 80.8 - - - +
414A ASP* 1.3 71.1 + - - +
415A VAL* 3.1 1.4 + - - +
439A ILE* 6.2 0.2 - - - +
441A ASP* 3.0 34.9 + - + +
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Residues in contact with ASP 414 (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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155A SER* 5.7 0.2 - - - -
177A PRO* 3.5 20.2 - - + +
179A ARG* 2.8 42.2 + - - -
266A LYS* 3.4 12.6 - - - +
380A GLY* 3.1 31.1 + - - +
381A LEU 3.2 4.3 + - - +
413A GLN* 1.3 72.4 - - - +
415A VAL* 1.3 59.3 + - - +
416A PHE* 3.6 22.9 - - + -
441A ASP 3.6 1.2 + - - -
442A HIS* 2.8 35.2 + - - -
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Residues in contact with VAL 415 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
368A LEU* 5.8 0.9 - - + -
378A VAL* 3.7 29.6 - - + +
379A ALA 4.5 0.9 - - - +
380A GLY 4.6 1.6 - - - +
381A LEU* 3.3 16.4 - - + +
383A VAL* 4.4 18.4 - - + -
394A VAL* 5.0 7.0 - - + -
412A LEU* 3.8 26.9 - - + -
413A GLN* 3.1 24.4 - - - +
414A ASP* 1.3 77.0 - - - +
416A PHE* 1.3 69.3 + - - +
417A VAL* 5.3 1.1 - - + -
431A ILE* 5.2 4.0 - - + -
442A HIS 3.6 2.6 + - - -
443A THR* 2.7 32.1 + - - +
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Residues in contact with PHE 416 (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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153A TRP* 4.2 8.7 - + - +
175A ALA* 3.7 40.2 - - + -
177A PRO* 4.0 14.1 - - + -
356A LEU* 3.6 34.3 - - + -
380A GLY* 5.6 1.1 - - - -
381A LEU 2.9 12.0 + - - +
382A LEU* 3.2 14.6 - - + +
383A VAL* 2.7 34.0 + - - +
414A ASP* 3.6 41.5 - - + -
415A VAL* 1.3 80.3 - - - +
417A VAL* 1.3 58.5 + - - +
442A HIS* 4.0 11.7 - + - -
444A TRP* 3.3 19.7 - - + +
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Residues in contact with VAL 417 (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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153A TRP* 5.7 0.9 + - - -
382A LEU* 4.2 0.9 - - - -
383A VAL* 3.3 20.4 - - + +
393A LEU* 3.7 28.3 - - + -
394A VAL* 4.7 7.4 - - + -
415A VAL* 4.3 1.3 - - + -
416A PHE* 1.3 78.0 - - - +
418A ARG* 1.3 64.6 + - - +
419A ILE* 4.0 9.6 - - + -
430A SER* 3.7 16.4 - - - +
431A ILE* 4.1 32.5 - - + -
444A TRP* 2.8 11.3 + - - +
445A VAL* 4.1 12.3 - - + -
446A TRP* 2.9 27.3 + - - +
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Residues in contact with ARG 418 (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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94A PHE* 3.6 16.9 - - - +
95A GLY 5.7 0.6 + - - -
98A ARG* 4.3 9.3 - - - +
118A TYR* 2.6 30.7 + - - -
153A TRP* 3.3 22.3 - - + -
382A LEU* 4.0 25.3 - - + +
383A VAL 3.0 7.6 + - - +
384A ASP* 2.9 39.3 + - - +
385A ALA 2.9 26.9 + - - -
417A VAL* 1.3 75.5 - - - +
419A ILE* 1.3 64.6 + - - +
420A GLY 3.0 25.8 + - - +
422A ALA* 4.4 11.9 - - - +
446A TRP* 3.3 30.1 - - + -
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Residues in contact with ILE 419 (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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385A ALA* 4.2 3.4 - - + -
393A LEU* 4.4 8.1 - - + -
417A VAL* 4.0 8.1 - - + -
418A ARG* 1.3 77.2 - - - +
420A GLY* 1.3 60.0 + - - +
425A GLY 3.1 31.2 - - - +
426A LYS* 3.6 11.4 - - - +
427A ALA* 4.1 2.0 - - + +
430A SER* 3.5 16.4 - - - +
446A TRP 3.0 21.3 + - - +
447A ARG* 3.8 5.6 - - - +
448A ALA 2.9 12.7 + - - -
459A ASN* 2.9 24.6 + - - +
461A ALA* 4.0 17.3 - - + -
482A PHE* 3.4 36.8 - - + -
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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