Contacts of the strand formed by residues 345 - 349 (chain A) in PDB entry 1JQP
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 MET 345 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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241A MET* 3.5 6.3 - - - -
245A ARG* 4.1 9.2 - - - +
323A VAL* 3.9 26.7 - - - -
335A MET* 3.2 29.8 - - - +
338A GLU* 3.8 6.7 - - + -
339A LEU* 3.3 34.1 - - + +
343A GLY 3.6 1.5 + - - +
344A PRO* 1.3 75.0 - - - +
346A ALA* 1.3 66.5 + - - +
347A VAL* 4.3 1.1 - - + -
383A LEU* 3.4 7.6 - - - +
384A LEU* 2.7 59.1 + - + -
429A ALA* 3.9 8.5 - - + -
430A MET 3.6 9.6 - - - +
431A ALA* 4.3 3.4 - - + -
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Residues in contact with ALA 346 (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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237A ALA* 4.5 12.6 - - + +
241A MET* 3.9 10.0 - - + -
278A PRO* 3.6 35.7 - - + -
345A MET* 1.3 73.1 - - - +
347A VAL* 1.3 62.5 + - - +
382A VAL 3.5 8.3 - - - +
383A LEU* 4.2 2.7 - - - +
428A ILE 4.8 0.7 - - - -
429A ALA* 3.2 5.5 - - - +
430A MET* 2.8 42.9 + - + +
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Residues in contact with VAL 347 (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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278A PRO* 6.0 1.6 - - - -
335A MET* 4.0 15.5 - - + -
345A MET* 4.3 0.9 - - + -
346A ALA* 1.3 81.4 - - - +
348A ALA* 1.3 60.1 + - - +
381A ALA* 3.5 3.9 - - - +
382A VAL* 2.9 54.0 + - + +
384A LEU* 4.0 30.3 - - + +
400A VAL* 4.7 1.8 - - + -
425A ILE* 4.0 25.8 - - + +
428A ILE 4.5 2.2 - - - -
429A ALA* 4.0 23.8 - - + +
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Residues in contact with ALA 348 (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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277A PHE* 6.1 5.8 - - + -
278A PRO* 6.1 3.4 - - + -
347A VAL* 1.3 75.0 - - - +
349A PHE* 1.3 65.8 + - - +
378A THR* 3.7 19.6 - - - +
380A HIS 3.0 17.0 - - - +
381A ALA* 4.5 5.4 - - + -
424A ALA 3.2 18.4 - - - +
425A ILE* 3.6 6.6 - - - -
428A ILE* 3.7 26.0 + - + +
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Residues in contact with PHE 349 (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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348A ALA* 1.3 78.9 - - - +
350A GLU* 1.3 82.3 + - - +
351A VAL* 3.7 18.8 + - + -
355A PHE* 3.7 41.7 - + - -
363A TYR* 5.2 1.3 - + - -
378A THR* 3.7 11.4 - - - +
379A ASN* 2.9 18.4 + - - +
380A HIS* 3.1 37.1 + + + +
382A VAL* 4.0 22.2 - - + -
414A PHE* 4.0 9.0 - + - -
416A ILE* 4.7 8.1 - - + -
423A CYS* 3.0 26.9 - - + +
425A ILE* 3.9 19.5 - - + -
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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