Contacts of the strand formed by residues 379 - 387 (chain T) in PDB entry 2P8Z
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 MET 379 (chain T).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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357T TYR* 3.3 39.7 - - + -
365T ASN* 3.7 29.4 - - + +
369T ILE* 3.4 31.9 - - + -
377T ASP 4.3 1.1 - - - +
378T LEU* 1.3 82.4 - - - +
380T LEU* 1.3 59.7 + - - +
381T TYR 4.1 0.2 - - - -
401T PHE* 2.8 30.0 + - + +
402T ALA* 3.1 20.6 + - + -
468T THR* 4.6 1.1 - - + -
469T LEU 3.5 2.0 - - - -
470T THR* 3.6 16.4 - - + -
475T ALA* 4.1 1.8 - - - -
476T HIS 3.6 11.0 - - - +
478T MET* 4.1 18.8 - - + -
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Residues in contact with LEU 380 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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378T LEU* 3.8 12.3 - - + -
379T MET* 1.3 71.9 - - - +
381T TYR* 1.3 76.7 + - - +
382T VAL* 3.8 9.0 + - + -
398T GLY* 4.6 4.0 - - - +
399T ARG 3.5 20.9 - - - +
400T VAL* 4.2 11.7 - - + +
405T VAL* 4.0 28.5 - - + -
454T ILE* 4.4 4.3 - - + -
456T LEU* 3.5 36.3 - - + -
468T THR* 3.5 3.1 - - - +
469T LEU* 2.7 50.7 + - + +
478T MET* 4.9 2.0 - - - -
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Residues in contact with TYR 381 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117T ALA* 4.8 7.2 - - - +
120T ARG* 3.8 42.3 + - + -
121T VAL* 4.9 6.5 - - + -
356T LEU* 6.4 0.7 - - + -
379T MET 4.0 2.0 + - - -
380T LEU* 1.3 73.0 - - - +
382T VAL* 1.3 64.6 + - - +
383T SER* 3.5 26.5 + - - -
398T GLY* 3.1 5.4 - - - -
399T ARG 3.0 32.0 + - - +
401T PHE* 3.7 26.9 - + + -
466T THR* 3.6 22.6 - - + +
467T GLY 3.5 18.6 - - - -
468T THR* 4.7 0.9 - - - +
478T MET* 3.8 28.9 - - + -
479T LYS* 3.9 18.1 + - - -
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Residues in contact with VAL 382 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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380T LEU* 3.8 9.8 + - + -
381T TYR* 1.3 73.3 - - - +
383T SER* 1.3 62.9 + - - +
384T LYS 3.9 12.1 - - - +
385T MET* 4.6 2.5 - - - -
396T ALA* 4.2 22.7 - - + -
397T PHE 3.5 10.8 - - - +
398T GLY* 4.3 0.2 - - - -
456T LEU* 4.9 2.2 - - + -
459T ILE* 5.4 0.9 - - + -
463T LEU* 3.7 27.4 - - + -
465T LYS 3.4 19.7 - - - +
466T THR* 3.2 21.0 - - - +
467T GLY 3.4 11.6 + - - +
469T LEU* 3.8 20.0 - - + -
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Residues in contact with SER 383 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117T ALA* 3.0 40.8 + - - +
118T ALA* 4.0 3.6 + - - -
121T VAL* 4.0 16.8 - - - +
381T TYR* 3.5 14.3 + - - -
382T VAL* 1.3 73.0 - - - +
384T LYS* 1.3 64.4 + - - +
397T PHE* 2.7 34.1 + - - -
398T GLY* 4.3 0.7 - - - -
465T LYS* 5.3 0.2 - - - -
466T THR* 3.6 16.7 - - - +
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Residues in contact with LYS 384 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65S THR* 4.5 8.7 + - - -
67S HIS* 3.2 33.0 + - - -
71T LYS* 5.9 3.0 - - - +
73T THR* 4.3 12.3 + - - -
106T PRO* 5.1 8.3 - - - +
114T GLU* 5.9 2.9 - - + +
117T ALA* 5.6 2.2 - - + -
382T VAL* 3.5 4.8 - - - +
383T SER* 1.3 83.3 - - - +
385T MET* 1.3 72.5 + - - +
386T VAL* 5.1 8.5 - - - -
387T PRO* 6.4 0.7 - - - -
396T ALA* 3.8 1.6 - - - -
397T PHE* 2.9 39.6 + - + +
465T LYS* 4.2 12.3 - - - +
516T PRO* 5.2 15.7 - - + -
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Residues in contact with MET 385 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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382T VAL* 4.6 6.3 - - - -
384T LYS* 1.3 84.7 - - - +
386T VAL* 1.3 60.2 + - - +
387T PRO* 4.0 5.2 - - - +
394T PHE* 2.9 57.6 - - + +
395T TYR 3.3 12.3 - - - -
396T ALA* 3.5 21.8 - - + +
459T ILE 5.0 1.1 - - - +
460T ASP* 4.0 15.9 - - - +
463T LEU* 3.5 25.4 - - - +
464T LEU* 4.0 5.4 - - + -
465T LYS* 3.6 26.3 - - - +
513T LYS 4.5 7.8 - - - +
514T SER 4.9 6.6 - - - +
516T PRO* 6.1 0.6 - - - +
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Residues in contact with VAL 386 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70T ILE* 5.0 5.6 - - + -
71T LYS* 4.4 13.9 - - + +
73T THR* 4.0 20.0 - - - +
384T LYS* 5.1 9.9 - - - +
385T MET* 1.3 73.8 - - - +
387T PRO* 1.3 84.3 - - + +
388T THR* 3.5 2.3 - - + +
394T PHE* 3.3 6.0 - - - -
395T TYR* 2.8 46.3 + - + +
397T PHE* 4.4 8.1 - - + -
437T MET* 3.2 32.8 - - + -
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Residues in contact with PRO 387 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70T ILE* 4.4 0.7 - - - -
71T LYS* 3.8 28.4 + - + +
384T LYS* 6.4 0.4 - - - -
385T MET 4.0 5.4 - - - +
386T VAL* 1.3 102.6 - - + +
388T THR* 1.3 61.2 + - - +
394T PHE* 4.1 27.8 - - + -
514T SER* 4.7 12.6 - - - +
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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