Contacts of the strand formed by residues 359 - 366 (chain D) in PDB entry 3B60
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 LEU 359 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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344D PHE* 6.3 1.6 - - + -
347D VAL* 5.1 2.2 - - + +
348D THR* 3.2 3.7 - - - +
349D PHE* 2.5 44.9 + - + +
357D PRO* 3.2 1.8 - - - +
358D ALA* 1.3 87.6 - - - +
360D ARG* 1.3 65.0 + - - +
362D ILE* 4.4 15.7 - - + -
381D GLY* 3.6 21.1 - - - +
384D THR* 3.3 31.6 - - + -
385D ILE* 3.8 21.8 - - + +
388D LEU* 3.9 17.0 - - + -
551D VAL* 5.5 4.7 - - + -
554D GLY 3.2 18.6 - - - +
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Residues in contact with ARG 360 (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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347D VAL 2.4 27.9 - - - +
348D THR* 3.6 11.0 - - + -
356D VAL* 4.4 19.0 - - - +
357D PRO* 4.3 25.1 + - + +
359D LEU* 1.3 73.9 - - - +
361D ASN* 1.3 60.6 + - - +
362D ILE* 2.6 14.5 + - - +
553D ASP* 4.3 24.2 + - - -
554D GLY* 3.0 13.5 + - - +
555D ILE* 4.2 25.1 - - + +
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Residues in contact with ASN 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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346D ASN* 3.5 30.7 - - + +
347D VAL 4.0 0.9 - - - -
348D THR* 3.6 12.0 + - - -
360D ARG* 1.3 78.8 - - + +
362D ILE* 1.3 66.2 + - - +
363D ASN* 3.8 13.1 + - - +
397D GLU* 5.5 1.2 - - - +
555D ILE* 4.3 11.9 - - + +
556D ILE* 4.6 3.1 - - - +
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Residues in contact with ILE 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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344D PHE* 3.6 26.4 - - + +
345D ARG 3.6 1.9 - - - -
346D ASN 3.2 1.6 + - - -
347D VAL* 3.1 31.1 + - + +
359D LEU* 4.4 16.8 - - + -
360D ARG 2.6 25.0 + - - +
361D ASN* 1.3 76.6 - - - +
363D ASN* 1.3 69.0 - - - +
364D LEU* 4.9 4.0 - - + -
385D ILE* 5.4 4.7 - - + -
549D VAL* 6.5 0.2 - - + -
551D VAL* 5.2 1.6 - - + -
554D GLY 4.1 3.6 - - - +
555D ILE* 3.6 13.2 - - + -
556D ILE* 3.0 49.8 - - + +
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Residues in contact with ASN 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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344D PHE 3.3 4.7 - - - -
345D ARG* 3.4 13.0 - - + +
346D ASN* 2.4 35.9 + - - +
361D ASN* 3.8 16.0 + - - +
362D ILE* 1.3 75.4 - - - +
364D LEU* 1.3 66.2 + - - +
556D ILE* 4.2 11.0 - - - +
559D ARG* 3.2 34.2 + - - +
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Residues in contact with LEU 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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342D LEU* 4.4 0.4 - - - +
343D GLU* 3.6 0.9 - - - -
344D PHE* 2.7 64.3 + - + +
345D ARG* 4.5 3.1 + - - +
362D ILE* 4.9 4.5 - - + -
363D ASN* 1.3 79.5 - - - +
365D LYS* 1.3 81.4 + - - +
366D ILE* 4.4 11.9 - - + -
372D VAL* 4.3 12.1 - - + -
374D LEU* 4.8 4.9 - - + -
385D ILE* 4.7 11.4 - - + -
547D GLU* 4.4 11.7 - - - +
549D VAL* 3.8 37.9 - - + -
556D ILE* 5.3 2.0 - - + -
559D ARG* 4.6 14.6 - - - +
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Residues in contact with LYS 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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341D ASP* 4.1 8.0 + - - -
342D LEU 3.7 2.7 - - - +
343D GLU* 3.1 34.4 + - + +
345D ARG* 3.8 18.7 - - - +
364D LEU* 1.3 86.6 - - - +
366D ILE* 1.3 66.8 + - - +
367D PRO* 3.3 30.5 - - + +
372D VAL* 4.3 4.2 - - - +
547D GLU* 5.3 4.0 - - - +
559D ARG* 5.2 2.0 - - - +
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Residues in contact with ILE 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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340D GLY 3.2 2.9 - - - +
342D LEU* 2.8 69.2 + - + +
344D PHE* 5.9 0.2 - - + -
364D LEU* 4.4 10.5 - - + -
365D LYS* 1.3 75.0 - - - +
367D PRO* 1.3 63.5 - - - +
370D LYS 4.1 9.9 - - - +
372D VAL* 3.4 35.2 - - + +
385D ILE* 6.1 2.5 - - + -
389D ILE* 6.1 0.2 - - + -
531D THR* 3.4 23.3 - - + +
532D SER 4.5 4.0 - - - +
533D LEU* 3.5 30.7 - - + -
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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