Contacts of the strand formed by residues 397 - 403 (chain A) in PDB entry 2X7Z
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 397 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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322A LEU 3.6 3.6 - - - +
323A ILE* 3.8 37.7 - - + -
375A ASN* 4.1 11.3 + - - +
395A SER* 3.4 11.9 - - - +
396A ASP* 1.3 88.2 - - + +
398A VAL* 1.3 62.9 + - - +
399A TYR* 5.6 5.0 - - + -
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Residues in contact with VAL 398 (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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320A ILE 3.6 1.7 - - - +
321A LYS* 3.5 4.4 - - - +
322A LEU* 2.9 37.6 + - + +
324A LYS* 4.5 1.1 - - + -
329A LEU* 3.9 27.8 - - + -
374A VAL* 4.0 6.1 - - + -
375A ASN* 3.4 4.0 - - - +
394A THR* 3.6 39.7 - - + +
395A SER 3.7 9.0 - - - +
396A ASP 4.3 3.4 - - - +
397A PHE* 1.3 81.2 - - - +
399A TYR* 1.3 61.6 + - - +
400A LEU* 3.7 30.7 - - + -
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Residues in contact with TYR 399 (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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319A GLU* 3.7 31.6 - - + -
320A ILE 3.6 4.0 - - - -
321A LYS* 3.8 26.9 - - + +
373A ALA 4.0 0.5 - - - +
374A VAL* 3.5 2.8 - - - -
375A ASN* 2.7 60.7 + - + +
397A PHE* 5.6 5.2 - - + -
398A VAL* 1.3 73.9 - - - +
400A LEU* 1.3 63.9 + - - +
401A LYS 4.3 0.2 + - - -
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Residues in contact with LEU 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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318A MET 3.6 0.7 - - - +
319A GLU* 3.3 6.2 - - - +
320A ILE* 2.8 47.4 + - + +
322A LEU* 4.0 20.6 - - + -
331A PHE* 3.8 35.0 - - + -
365A LEU* 4.3 18.6 - - + -
371A LEU* 4.0 19.7 - - + -
373A ALA 3.6 1.8 - - - -
374A VAL* 4.3 13.5 - - + -
391A LEU* 4.4 2.7 - - + -
398A VAL* 3.7 25.1 - - + -
399A TYR* 1.3 76.4 - - - +
401A LYS* 1.3 60.6 + - - +
402A VAL* 4.2 7.0 - - + -
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Residues in contact with LYS 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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317A ILE* 3.5 37.0 - - + +
318A MET 3.5 4.9 - - - +
319A GLU* 4.7 6.1 - - + +
371A LEU* 3.7 2.3 - - - +
372A LEU* 2.8 44.4 + - + +
373A ALA* 3.0 35.9 + - + +
380A GLU* 4.7 6.1 + - - -
399A TYR 4.3 0.2 + - - -
400A LEU* 1.3 70.6 - - - +
402A VAL* 1.3 64.4 + - - +
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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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316A LYS 3.9 0.2 - - - +
317A ILE* 3.4 3.5 - - - -
318A MET* 2.9 37.9 + - + +
320A ILE* 4.0 16.6 - - + -
350A VAL* 5.8 0.2 - - + -
365A LEU* 3.7 21.3 - - + -
369A ASP* 3.4 39.3 - - + +
370A LYS 3.2 10.3 - - - +
371A LEU* 4.1 14.4 - - + -
372A LEU* 4.3 5.2 - - - -
400A LEU* 4.2 9.6 - - + +
401A LYS* 1.3 80.5 - - - +
403A ALA* 1.3 65.1 + - - +
404A LYS* 4.0 4.8 + - + -
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Residues in contact with ALA 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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315A GLU* 3.7 33.4 - - + +
316A LYS 3.6 4.9 - - - +
317A ILE* 4.6 2.2 - - + +
369A ASP* 4.0 3.5 - - - -
370A LYS* 2.8 48.7 + - + +
372A LEU* 3.9 21.2 - - + +
402A VAL* 1.3 75.6 - - - +
404A LYS* 1.3 62.7 + - - +
405A PRO* 4.0 0.5 - - - +
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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