Contacts of the strand formed by residues 377 - 382 (chain A) in PDB entry 1JD7
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 GLY 377 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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348A PHE* 4.0 11.0 - - - -
352A THR* 4.1 4.1 - - - +
372A GLY* 3.3 2.3 - - - -
373A ARG 2.7 32.4 + - - -
374A GLY 3.6 5.0 - - - +
375A SER 3.5 2.0 - - - -
376A SER* 1.3 80.9 - - - +
378A HIS* 1.3 58.1 + - - +
396A MET* 3.3 11.8 - - - +
441A ILE 3.0 14.1 - - - -
442A HIS* 3.8 0.4 - - - -
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Residues in contact with HIS 378 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348A PHE* 3.6 4.6 - - - -
359A THR* 4.6 2.2 + - - -
360A ASN* 4.5 5.6 + - + -
370A SER* 3.0 26.4 + - - -
371A PHE* 3.5 23.5 + - - -
372A GLY* 3.4 12.3 - - - -
374A GLY 5.6 0.6 + - - -
377A GLY* 1.3 74.4 + - - -
379A MET* 1.3 76.9 + - - +
392A VAL* 3.9 8.0 - - + +
393A GLN 3.4 24.9 + - - -
394A THR* 3.3 32.8 - - + +
395A ASP 5.0 1.0 + - - -
396A MET* 3.8 4.7 - - - +
429A ILE* 4.6 0.7 - - + -
439A MET* 3.9 12.9 - - + +
440A ALA* 3.4 0.5 - - - -
441A ILE* 2.9 47.2 + - + +
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Residues in contact with MET 379 (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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289A VAL* 4.2 10.1 - - + +
290A PHE* 4.4 3.1 - - - -
293A ALA* 4.0 21.3 - - + -
348A PHE* 4.5 7.2 - - + -
369A ILE* 4.6 4.9 - - + +
370A SER* 2.8 23.1 + - - -
371A PHE* 2.9 67.9 + - + +
378A HIS* 1.3 77.8 - - - +
380A ALA* 1.3 70.6 + - - +
381A ILE* 3.5 34.8 - - + -
439A MET* 3.3 18.8 - - - +
440A ALA* 4.3 9.2 - - + -
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Residues in contact with ALA 380 (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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369A ILE 3.1 13.5 - - - +
370A SER* 3.7 11.4 - - - +
379A MET* 1.3 82.1 - - - +
381A ILE* 1.3 65.8 + - - +
388A LEU* 4.6 1.3 - - + -
431A LEU* 4.0 17.9 - - + -
433A ILE* 3.7 22.3 - - + +
438A ALA* 3.1 6.4 - - - +
439A MET* 3.0 31.4 + - + +
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Residues in contact with ILE 381 (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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233A PHE* 4.4 3.4 - - + -
238A LEU* 3.9 18.6 - - + +
286A LEU* 3.7 43.3 - - + +
289A VAL* 4.0 4.0 - - + -
290A PHE* 4.0 16.4 - - + +
367A ASN 4.0 0.9 - - - +
368A GLN* 3.4 4.5 - - - +
369A ILE* 2.8 48.9 + - + +
379A MET* 3.5 26.9 - - + -
380A ALA* 1.3 80.7 - - - +
382A ASN* 1.3 67.6 + - - +
383A LYS* 4.9 0.2 - - + -
388A LEU* 4.2 3.9 - - - +
437A ASP 3.9 8.3 - - - +
438A ALA* 3.8 10.8 - - + -
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Residues in contact with ASN 382 (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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286A LEU* 4.6 0.3 - - - +
367A ASN 3.9 1.3 - - - -
368A GLN* 3.0 24.3 + - - +
381A ILE* 1.3 73.8 - - - +
383A LYS* 1.3 61.3 + - - +
384A GLU* 2.9 18.6 + - - +
386A SER 3.0 19.2 + - - -
388A LEU* 3.5 15.8 - - + +
433A ILE* 2.8 32.4 + - + +
434A GLY 3.0 19.7 + - - +
435A ALA* 3.4 2.6 - - - +
436A TRP* 2.8 28.1 + - - -
437A ASP 3.0 11.8 + - - +
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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