Contacts of the strand formed by residues 386 - 391 (chain B) in PDB entry 2V4M
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 ARG 386 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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413A PRO* 3.4 30.3 - - - +
415A MET* 3.5 27.0 - - - +
384B CYS 3.8 0.8 - - - -
385B ARG* 1.3 80.6 + - - +
387B LEU* 1.3 79.2 + - - +
388B ILE* 3.4 13.6 - - + +
412B LEU* 4.4 3.9 - - - +
413B PRO* 3.5 21.5 - - + +
415B MET* 3.6 19.3 - - + +
427B THR* 5.6 0.4 - - - +
428B PRO 3.2 21.8 + - - -
430B PHE* 4.0 10.3 - - - -
432B ASP 3.8 3.2 + - - -
433B ASP* 2.8 44.1 + - - +
434B VAL* 2.9 27.7 + - - +
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Residues in contact with LEU 387 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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381B ILE* 5.0 3.6 - - + +
384B CYS* 5.7 0.2 - - + -
386B ARG* 1.3 81.8 - - - +
388B ILE* 1.3 63.2 + - - +
389B LEU* 4.2 3.8 - - + -
406B LEU* 4.4 10.3 - - + -
410B THR* 4.1 18.6 - - + +
412B LEU* 4.5 16.6 - - + -
413B PRO 3.0 12.6 + - - +
414B VAL* 3.4 24.4 - - + -
415B MET 2.8 25.8 + - - -
434B VAL* 3.3 24.5 - - + +
436B PHE* 4.0 15.7 - - + -
506B PHE* 3.9 29.4 - - + -
510B MET* 5.1 1.3 - - + -
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Residues in contact with ILE 388 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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386B ARG* 3.4 43.1 - - + +
387B LEU* 1.3 77.7 - - - +
389B LEU* 1.3 59.8 + - - +
390B ILE* 4.0 14.8 - - + +
415B MET* 3.3 33.2 - - + +
417B GLU* 3.9 13.0 - - + -
422B PHE* 4.4 2.0 - - + -
429B VAL* 4.3 11.4 - - + -
433B ASP* 4.0 11.4 - - + +
434B VAL 3.0 5.7 + - - +
435B CYS* 3.3 22.9 - - + +
436B PHE* 2.6 35.7 + - - +
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Residues in contact with LEU 389 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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387B LEU* 4.7 5.2 - - + -
388B ILE* 1.3 73.9 - - - +
390B ILE* 1.3 57.9 + - - +
391B ALA* 4.2 0.9 - - - -
396B TYR* 5.2 0.2 - - - -
399B GLY* 3.6 26.5 - - - +
402B THR* 4.7 0.4 - - - +
406B LEU* 4.0 26.7 - - + -
414B VAL* 4.0 13.5 - - + -
415B MET 2.8 14.8 + - - +
416B VAL* 3.5 28.9 - - + +
417B GLU 2.8 33.3 + - - +
436B PHE* 3.6 35.4 - - + -
438B LEU* 4.7 9.4 - - + -
503B LEU* 4.9 8.5 - - + -
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Residues in contact with ILE 390 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388B ILE* 4.0 15.0 - - + -
389B LEU* 1.3 75.3 - - - +
391B ALA* 1.3 68.7 + - - +
417B GLU* 3.5 6.1 - - + +
419B ALA* 3.8 27.4 - - + -
422B PHE* 3.3 50.9 - - + -
435B CYS* 4.8 4.0 - - + -
436B PHE 2.8 13.6 + - - +
437B PHE* 3.4 37.2 - - + -
438B LEU* 3.2 19.7 + - - +
447B THR* 3.8 7.2 - - - +
450B GLY* 5.0 2.7 - - - -
454B CYS* 3.7 8.1 - - - -
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Residues in contact with ALA 391 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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389B LEU 4.2 0.9 - - - -
390B ILE* 1.3 80.2 - - - +
392B CYS* 1.3 63.7 + - - +
395B SER 3.5 7.9 - - - +
396B TYR* 3.5 30.5 - - - +
417B GLU 3.2 10.1 + - - +
418B LEU* 3.4 4.9 - - - -
419B ALA 3.0 18.6 + - - -
438B LEU* 3.3 27.4 - - + +
447B THR* 3.9 7.9 - - - -
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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