Contacts of the strand formed by residues 360 - 368 (chain D) in PDB entry 3F7F
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 ALA 360 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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329D TRP* 4.2 14.4 - - + -
356D LYS* 3.5 5.7 - - - +
357D SER* 3.0 35.5 + - - +
358D GLY 3.2 0.6 - - - -
359D THR* 1.3 81.6 + - - +
361D SER* 1.3 60.4 + - - +
384D LYS* 6.6 0.4 - - - +
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Residues in contact with SER 361 (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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6D ARG* 4.2 13.6 + - - +
329D TRP* 4.0 7.2 - - - -
354D LEU* 4.5 6.0 - - - +
355D TRP 3.6 10.3 - - - -
356D LYS* 5.0 0.4 - - - -
359D THR 4.1 1.9 + - - -
360D ALA* 1.3 76.5 - - - +
362D LYS* 1.3 63.4 + - - +
383D ASN* 3.3 23.2 + - - +
458D ASN 6.1 0.2 - - - -
460D ALA* 4.1 24.9 - - - +
484D TYR* 3.6 19.2 + - - -
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Residues in contact with LYS 362 (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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322D ASN 5.5 1.2 + - - -
323D LEU* 3.9 23.6 - - + -
329D TRP* 3.8 38.1 - - + +
353D VAL 3.6 1.0 - - - +
354D LEU* 3.5 5.0 - - - +
355D TRP* 2.8 50.2 + - + +
361D SER* 1.3 77.7 - - - +
363D LEU* 1.3 62.3 + - - +
364D GLN* 4.2 7.0 - - + +
380D GLU* 2.7 32.1 + - - +
383D ASN* 3.5 16.8 - - - +
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Residues in contact with LEU 363 (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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4D LEU* 4.3 15.3 - - + -
352D ILE* 4.0 13.0 - - + -
353D VAL 3.3 6.1 - - - +
354D LEU* 4.2 20.4 - - + -
362D LYS* 1.3 75.5 - - - +
364D GLN* 1.3 75.1 + - - +
365D ILE* 4.9 1.6 - - + -
380D GLU* 5.1 0.2 - - - +
381D SER* 3.0 41.5 + - - +
383D ASN* 3.1 9.1 + - - +
463D ILE* 5.1 2.0 - - + -
471D ILE* 3.7 28.0 - - + -
473D VAL* 4.4 10.8 - - + -
484D TYR* 3.8 34.5 - - + -
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Residues in contact with GLN 364 (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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321D THR* 5.9 0.7 - - - -
322D ASN* 3.5 29.8 + - - +
323D LEU* 4.2 5.8 - - - +
352D ILE* 3.6 0.9 - - - -
353D VAL* 2.8 32.5 + - + +
355D TRP* 2.7 36.4 + - + +
362D LYS* 4.2 9.1 - - + +
363D LEU* 1.3 85.9 - - - +
365D ILE* 1.3 69.4 + - - +
366D LEU 4.3 0.2 - - - -
378D TRP* 3.8 23.2 - - + -
379D ILE 3.4 12.8 - - - +
380D GLU* 3.1 34.9 + - - +
381D SER* 5.9 0.2 - - - -
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Residues in contact with ILE 365 (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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4D LEU* 3.9 22.4 - - + -
340D LEU* 3.8 20.9 - - + -
342D LEU* 4.1 11.9 - - + -
350D ASN* 3.4 33.9 - - + +
351D LEU 3.2 9.4 - - - +
352D ILE* 4.2 8.1 - - + -
363D LEU* 4.9 2.5 - - + -
364D GLN* 1.3 80.9 - - - +
366D LEU* 1.3 61.6 + - - +
367D ASN 3.6 1.6 + - - -
378D TRP* 3.7 3.6 - - - -
379D ILE* 2.9 40.6 + - + +
471D ILE* 3.5 32.8 - - + -
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Residues in contact with LEU 366 (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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298D PHE* 5.1 1.6 - - + -
300D MET* 3.9 17.0 - - + -
319D ILE* 3.8 30.3 - - + -
349D LEU 3.9 0.2 - - - +
350D ASN* 3.4 5.5 - - - -
351D LEU* 2.7 55.3 + - + +
365D ILE* 1.3 71.2 - - - +
367D ASN* 1.3 62.1 + - - +
368D VAL* 3.9 13.6 + - + +
376D TYR* 3.8 21.1 - - + -
377D GLU 4.0 2.7 - - - +
378D TRP* 3.3 49.6 - - + +
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Residues in contact with ASN 367 (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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342D LEU* 4.1 21.7 - - + +
344D VAL* 4.5 16.5 + - - +
346D ALA 3.4 19.3 + - - -
347D SER* 2.8 33.3 + - - -
350D ASN* 3.2 13.9 - - - +
365D ILE 3.6 0.8 + - - -
366D LEU* 1.3 72.2 - - - +
368D VAL* 1.3 61.7 + - - +
369D ASN* 4.4 6.7 + - - +
376D TYR* 3.2 4.7 - - - +
377D GLU* 2.8 50.6 + - - +
379D ILE* 4.8 6.0 - - + +
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Residues in contact with VAL 368 (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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300D MET* 4.4 22.4 - - - -
319D ILE* 4.5 3.1 - - + -
336D LEU* 6.5 0.7 - - + -
347D SER* 3.6 1.4 - - - -
348D TYR* 2.8 41.3 + - + -
349D LEU* 3.2 43.1 + - + +
351D LEU* 6.3 0.7 - - + -
366D LEU* 4.4 14.4 - - + +
367D ASN* 1.3 74.4 - - - +
369D ASN* 1.3 55.4 + - - +
370D ASP 4.6 5.2 - - - +
373D PHE* 4.7 13.2 - - + -
375D ASN 3.8 6.1 - - - +
376D TYR* 4.0 11.2 - - + -
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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