Contacts of the strand formed by residues 387 - 391 (chain B) in PDB entry 2AG1
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 VAL 387 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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382B HIS* 3.4 24.7 - - + +
383B VAL* 4.5 4.9 - - + -
384B ASP* 2.8 19.2 + - - +
385B ALA 3.2 1.2 + - - -
386B GLY* 1.3 85.0 - - - +
388B THR* 1.3 77.0 + - - +
389B VAL* 4.0 12.3 - - + -
409B PRO* 3.8 3.8 - - - +
410B GLY 2.8 29.3 + - - -
411B GLY 3.4 1.8 + - - +
440B ARG* 4.4 2.5 - - - -
441B ARG* 3.2 16.8 - - + +
443B ILE* 3.8 21.8 - - + -
532B LEU* 5.8 3.8 - - + -
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Residues in contact with THR 388 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63B ALA* 4.5 4.5 - - + +
387B VAL* 1.3 74.9 - - - +
389B VAL* 1.3 63.5 + - - +
390B VAL* 4.1 14.8 - - + -
411B GLY* 3.4 21.9 + - - +
413B LEU* 4.3 9.2 - - + -
431B ALA* 4.3 9.4 - - + -
435B ASP* 3.1 35.7 + - - +
440B ARG* 3.5 12.9 + - - +
441B ARG 2.8 8.5 + - - +
442B THR* 3.3 6.0 - - + +
443B ILE 2.8 31.2 + - - +
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Residues in contact with VAL 389 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
379B ILE* 5.4 3.4 - - + -
383B VAL* 4.0 34.1 - - + -
387B VAL* 4.0 10.5 - - + -
388B THR* 1.3 75.9 - - - +
390B VAL* 1.3 65.7 + - - +
400B LEU* 4.0 24.0 - - + -
404B MSE 4.4 8.7 - - + -
409B PRO* 4.8 0.4 - - + -
411B GLY 2.9 10.1 + - - +
412B PHE* 3.3 25.0 - - + -
413B LEU 2.8 24.1 + - - -
443B ILE* 3.5 7.6 - - + +
445B VAL* 4.2 14.1 - - + -
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Residues in contact with VAL 390 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388B THR* 4.1 8.3 - - + -
389B VAL* 1.3 79.3 - - - +
391B ALA* 1.3 58.6 + - - +
413B LEU* 3.3 21.3 - - + +
424B GLY* 3.8 17.3 - - - +
427B THR* 3.9 16.8 - - + -
428B ALA* 3.7 27.6 - - + +
431B ALA* 4.5 0.7 - - + -
442B THR* 3.9 14.6 - - + -
443B ILE 2.8 10.7 + - - +
444B LEU* 3.4 16.5 - - + +
445B VAL* 2.7 35.0 + - - +
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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 VAL 4.2 0.2 - - - -
390B VAL* 1.3 75.5 - - - +
392B ASP* 1.3 59.9 + - - +
396B THR* 6.0 0.2 - - + -
397B TYR* 3.9 9.9 - - + -
400B LEU* 3.8 26.5 - - + -
412B PHE* 4.3 8.1 - - + -
413B LEU 2.8 17.3 + - - +
414B CYS* 3.8 32.4 - - - -
415B HIS* 4.0 8.3 + - - -
424B GLY* 5.2 2.1 - - - -
444B LEU* 4.7 1.3 - - - -
445B VAL 3.2 4.5 - - - +
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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