Contacts of the strand formed by residues 411 - 418 (chain D) in PDB entry 1TYE
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 GLU 411 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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409D GLU* 5.2 0.5 - - - +
410D LYS* 1.3 85.2 + - + +
412D LYS* 1.3 91.1 + - - +
413D SER* 5.1 0.5 - - - -
428D GLN* 3.9 20.6 + - - +
429D VAL 3.9 3.7 - - - +
430D THR* 4.0 17.3 + - - +
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Residues in contact with LYS 412 (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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361D ASP* 6.2 3.1 - - - +
363D PRO* 4.3 20.4 - - + +
409D GLU* 3.2 40.8 + - + +
410D LYS 4.2 0.2 - - - -
411D GLU* 1.3 91.0 - - - +
413D SER* 1.3 77.6 + - - +
428D GLN* 3.6 0.2 - - - -
429D VAL* 3.1 39.6 + - + +
431D PHE* 6.4 0.2 - - + -
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Residues in contact with SER 413 (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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361D ASP* 3.8 13.7 - - - +
363D PRO* 5.3 2.0 - - - +
411D GLU* 5.1 0.7 - - - -
412D LYS* 1.3 90.1 - - - +
414D PHE* 1.3 66.6 + - - +
426D ILE* 4.4 10.5 - - - +
427D VAL 3.1 15.7 - - - -
428D GLN* 4.0 15.9 - - - -
429D VAL* 4.5 0.9 - - - +
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Residues in contact with PHE 414 (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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90D LEU* 4.8 3.1 - - + -
100D PHE* 5.0 2.2 - + - -
359D VAL* 4.7 3.1 - - + -
360D ARG 3.4 3.4 - - - +
361D ASP* 2.5 33.4 - - - +
362D LEU* 4.1 18.2 - - + -
363D PRO* 4.3 8.5 - - + -
366D LEU* 4.1 9.9 - - + -
368D LEU* 3.9 31.4 - - + -
413D SER* 1.3 74.0 - - - +
415D THR* 1.3 72.9 + - - +
416D ILE* 4.0 9.2 - - + -
426D ILE* 3.4 6.8 - - - +
427D VAL* 2.9 75.2 + - + -
429D VAL* 3.8 20.9 - - + -
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Residues in contact with THR 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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358D GLU 3.8 0.5 - - - +
359D VAL* 3.9 1.4 - - - -
360D ARG* 3.1 52.2 + - - +
361D ASP* 3.5 8.3 + - - -
414D PHE* 1.3 80.9 + - - +
416D ILE* 1.3 74.3 + - - +
417D LYS* 4.1 0.7 - - + -
424D SER* 3.4 30.1 - - - +
425D LEU 3.2 11.4 - - - +
426D ILE* 4.4 11.8 - - + +
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Residues in contact with ILE 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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83D VAL* 5.4 0.3 - - - +
100D PHE* 4.3 23.8 - - + -
102D ILE* 4.5 13.4 - - + +
357D LEU* 4.2 35.4 - - + -
358D GLU 3.7 7.0 - - - +
359D VAL* 5.1 5.2 - - + -
368D LEU* 4.3 15.7 - - + -
370D PHE* 4.7 7.4 - - + -
399D ILE* 4.6 7.9 - - + -
414D PHE* 4.0 24.5 - - + -
415D THR* 1.3 79.1 - - - +
417D LYS* 1.3 60.4 + - - +
418D PRO* 4.5 2.4 - - - +
424D SER* 3.9 0.7 - - - -
425D LEU* 2.9 41.3 + - + +
427D VAL* 4.4 4.3 - - + -
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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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357D LEU* 4.4 2.0 - - - -
358D GLU* 3.1 52.3 + - - +
360D ARG* 4.1 27.6 - - - +
415D THR* 4.1 1.7 - - + -
416D ILE* 1.3 75.1 - - - +
418D PRO* 1.3 76.3 + - + +
420D GLY 4.4 5.9 - - - +
421D PHE 3.0 29.1 + - - +
422D LYS* 4.8 4.3 - - - +
423D ASP 3.5 7.9 - - - +
424D SER* 3.4 27.4 - - - -
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Residues in contact with PRO 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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83D VAL* 4.4 9.4 - - + -
102D ILE* 6.1 0.9 - - + -
104D VAL* 4.1 12.8 - - + -
355D VAL* 3.9 24.7 - - + -
356D GLU 3.3 12.8 - - - +
357D LEU* 4.1 12.1 - - + -
416D ILE 4.5 1.8 - - - +
417D LYS* 1.3 92.3 + - + +
419D VAL* 1.3 66.3 + - - +
420D GLY 3.1 0.3 + - - -
421D PHE* 3.0 52.8 + - + +
423D ASP 3.8 9.0 - - - +
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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