Contacts of the strand formed by residues 399 - 404 (chain A) in PDB entry 3PEY
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 399 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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332A SER* 3.3 8.3 - - - +
334A ILE* 4.1 20.2 - - + -
376A PHE* 3.8 27.4 - - + -
394A ILE* 6.4 0.2 - - + -
396A ILE* 3.0 36.1 + - + +
397A PRO 3.2 5.4 - - - +
398A THR* 1.3 73.1 - - - +
400A SER* 1.3 55.2 + - - +
401A MET 3.9 17.0 - - - +
402A VAL* 4.3 2.2 - - + -
426A ARG* 3.6 24.3 - - + +
427A THR* 2.7 27.7 + - - -
428A GLY 4.4 1.2 + - - -
433A LYS 5.4 0.5 - - - +
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Residues in contact with SER 400 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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330A ILE* 2.6 33.6 + - - -
331A GLY* 5.0 0.2 - - - -
332A SER 2.9 5.0 + - - -
398A THR 3.0 6.7 + - - -
399A VAL* 1.3 73.0 - - - +
401A MET* 1.3 63.7 + - - +
427A THR* 3.3 10.2 + - - -
433A LYS 5.2 1.8 - - - -
434A GLY* 3.7 1.8 - - - -
435A VAL* 3.0 25.5 + - - +
480A LEU* 3.8 32.7 - - - +
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Residues in contact with MET 401 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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324A LEU* 4.3 9.2 - - + -
327A LEU* 4.4 14.4 - - + +
328A MET* 3.9 26.0 - - + -
332A SER 3.5 1.8 + - - -
333A SER* 3.2 15.9 - - - +
334A ILE 3.0 23.4 + - - -
399A VAL* 3.7 3.3 - - - +
400A SER* 1.3 83.1 + - - +
402A VAL* 1.3 70.2 + - - +
403A VAL* 4.0 23.8 - - + -
435A VAL* 3.2 17.3 - - + +
437A ILE* 4.1 15.9 - - + -
476A VAL* 4.1 37.2 - - + -
480A LEU* 5.8 1.3 - - + -
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Residues in contact with VAL 402 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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334A ILE* 3.4 6.1 - - + +
336A PHE* 3.7 24.7 - - + -
399A VAL* 4.3 4.0 - - + -
401A MET* 1.3 78.4 - - - +
403A VAL* 1.3 68.0 + - - +
404A ASN* 4.7 2.9 + - - +
423A ARG* 3.6 33.0 - - + +
424A ILE* 4.0 22.9 - - + +
426A ARG* 4.0 16.6 - - + -
427A THR* 4.0 9.6 - - + +
435A VAL 2.9 9.4 + - - +
436A ALA* 3.2 4.5 - - + +
437A ILE 2.8 26.2 + - - +
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Residues in contact with VAL 403 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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321A LEU* 4.4 9.9 - - + -
324A LEU* 4.0 7.2 - - + -
328A MET* 3.9 26.7 - - + -
333A SER* 5.7 0.7 - - - -
334A ILE 2.8 15.8 + - - +
335A ILE* 4.3 7.4 - - + -
336A PHE* 2.8 31.0 + - - +
401A MET* 4.0 16.4 - - + -
402A VAL* 1.3 76.9 - - - +
404A ASN* 1.3 63.0 + - - +
405A TYR* 3.2 15.7 + - + +
437A ILE* 3.2 11.9 - - + +
439A PHE* 4.0 26.2 - - + -
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Residues in contact with ASN 404 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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336A PHE* 4.1 4.2 - - - +
402A VAL* 5.0 1.3 - - - +
403A VAL* 1.3 71.3 - - - +
405A TYR* 1.3 64.0 + - - +
406A ASP 3.3 14.5 - - - +
407A LEU* 4.2 7.2 - - + +
408A PRO* 4.5 1.6 - - - -
420A TYR* 3.5 25.1 - - - -
423A ARG* 3.0 38.7 + - - +
424A ILE* 3.8 14.7 - - - +
436A ALA* 5.4 0.8 - - - +
437A ILE 2.8 9.7 + - - -
438A SER* 2.9 28.7 + - - +
439A PHE* 3.0 25.6 + - - +
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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