Contacts of the strand formed by residues 394 - 402 (chain T) in PDB entry 2P8W
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 PHE 394 (chain T).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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385T MET* 2.9 43.6 - - + +
386T VAL 3.3 19.5 - - - +
387T PRO* 4.1 22.7 - - + -
388T THR 5.8 0.2 - - - -
392T GLY* 3.5 20.9 - - - -
393T ARG* 1.3 79.0 - - - +
395T TYR* 1.3 61.4 + - - +
396T ALA 4.0 0.2 + - - -
456T LEU 5.0 0.2 - - - +
460T ASP* 2.6 34.7 + - + +
464T LEU* 6.1 5.2 - - + -
510T ARG* 5.3 12.3 - - + -
513T LYS* 3.7 47.1 - - + -
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Residues in contact with TYR 395 (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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68T ILE* 5.6 6.2 - - + +
385T MET* 3.3 2.8 - - - +
386T VAL* 2.8 50.7 + - + +
388T THR* 3.5 28.9 - - + -
390T ASP* 3.9 20.1 + - + +
393T ARG* 4.5 13.5 - - + -
394T PHE* 1.3 77.6 - - - +
396T ALA* 1.3 61.8 + - - +
435T VAL* 4.5 13.0 - - + -
437T MET* 4.4 7.4 - - + -
442T VAL* 4.3 34.8 - - + +
456T LEU 3.6 10.8 - - - +
457T VAL* 4.1 32.8 - - + +
460T ASP* 5.0 1.6 - - - -
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Residues in contact with ALA 396 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
382T VAL* 4.2 20.9 - - + -
384T LYS 3.8 0.4 - - - -
385T MET* 3.5 23.5 - - - +
394T PHE 4.0 0.2 + - - -
395T TYR* 1.3 72.6 - - - +
397T PHE* 1.3 61.4 + - - +
437T MET* 4.3 1.2 - - - +
454T ILE 4.0 0.2 - - - +
455T GLY* 3.2 5.2 - - - -
456T LEU* 2.7 52.3 + - + +
459T ILE* 4.1 18.2 - - + -
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Residues in contact with PHE 397 (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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67S HIS* 5.8 1.1 - + - -
73T THR* 5.1 18.8 - - + -
74T ALA* 6.2 4.3 - - + -
103T ILE* 5.5 7.9 - - + -
118T ALA* 6.3 1.1 - - - -
121T VAL* 4.4 19.7 - - + -
382T VAL* 3.5 5.1 - - - -
383T SER* 2.7 51.4 + - - -
384T LYS* 2.9 36.8 + - + +
386T VAL* 4.4 6.7 - - + -
395T TYR 3.6 0.6 + - - -
396T ALA* 1.3 73.9 - - - +
398T GLY* 1.3 56.9 + - - +
437T MET* 4.0 38.4 - - + -
453T ILE* 3.4 39.0 - - + -
454T ILE 3.8 2.9 - - - -
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Residues in contact with GLY 398 (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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121T VAL* 5.3 2.0 - - - -
380T LEU* 4.6 7.1 - - - +
381T TYR 3.1 13.7 - - - -
382T VAL* 4.3 0.9 - - - -
383T SER* 3.8 9.0 - - - -
396T ALA 4.2 0.2 + - - -
397T PHE* 1.3 82.0 - - - +
399T ARG* 1.3 61.1 + - - +
453T ILE* 3.4 9.9 - - - +
454T ILE* 2.9 34.9 + - - -
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Residues in contact with ARG 399 (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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21T ASN* 5.3 3.2 + - - -
120T ARG 4.2 5.9 + - - -
121T VAL* 4.2 25.0 + - + +
123T ASP* 4.1 16.8 + - - -
345T PRO* 3.8 20.2 - - - +
348T ALA* 5.3 1.0 - - - +
349T GLN* 2.9 38.4 + - - +
352T ARG* 3.6 20.4 - - - +
380T LEU* 4.2 3.9 - - - +
381T TYR* 3.0 32.1 + - + +
398T GLY* 1.3 75.3 - - - +
400T VAL* 1.3 70.8 + - - +
401T PHE* 3.3 39.0 + - + -
451T GLY 4.6 6.2 + - - -
452T ASN 3.5 13.5 - - - +
453T ILE* 4.1 20.3 - - + +
454T ILE 4.8 0.2 - - - +
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Residues in contact with VAL 400 (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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349T GLN* 4.3 0.2 - - - +
378T LEU* 4.2 8.3 - - + -
379T MET 4.1 2.0 - - - -
380T LEU* 4.2 9.4 - - + -
399T ARG* 1.3 71.5 - - - +
401T PHE* 1.3 56.3 + - - +
402T ALA 3.4 22.4 - - - +
403T GLY 3.5 18.4 - - - +
405T VAL* 4.2 9.2 - - + -
448T CYS* 3.9 33.0 - - - +
449T PRO 3.8 9.2 - - - +
450T ALA* 3.5 8.3 - - - +
451T GLY* 2.7 33.6 + - - -
452T ASN 3.0 7.5 + - - +
454T ILE* 4.0 16.4 - - + -
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Residues in contact with PHE 401 (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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120T ARG* 5.1 5.4 - - + -
121T VAL* 6.3 0.9 - - + -
349T GLN* 3.1 44.3 + - + -
352T ARG* 4.0 9.2 - - - -
356T LEU* 3.5 35.4 - - + -
368T ALA 3.9 1.4 - - - +
369T ILE* 3.4 20.8 - - + -
372T CYS* 3.8 5.2 - - - -
379T MET 2.8 13.9 + - - +
381T TYR* 3.7 24.0 - + + -
399T ARG* 3.3 59.0 + - + -
400T VAL* 1.3 74.1 - - - +
402T ALA* 1.3 61.7 + - - +
450T ALA* 3.6 9.7 - - - +
478T MET* 3.6 21.8 - - + -
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Residues in contact with ALA 402 (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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368T ALA* 3.8 23.1 - - + +
369T ILE* 3.7 9.4 - - + -
373T ASP 3.6 5.2 - - - -
377T ASP 3.6 11.0 - - - +
378T LEU* 3.4 8.5 - - - +
379T MET* 3.1 40.6 + - + -
400T VAL* 3.4 2.4 - - - +
401T PHE* 1.3 80.2 - - - +
403T GLY* 1.3 67.7 + - - +
450T ALA* 3.8 2.0 - - - -
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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