Contacts of the strand formed by residues 404 - 412 (chain A) in PDB entry 3IJE
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 404 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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363A PRO* 3.1 21.9 + - - +
370A LYS 3.2 21.2 + - - +
371A GLY* 3.5 18.8 - - - -
372A ILE 4.1 1.0 + - - +
373A VAL* 3.4 24.2 - - + -
391A LEU* 3.9 16.8 - - + -
392A GLU 4.1 4.3 - - - -
393A GLY* 3.8 14.4 - - - -
394A GLN 5.0 1.3 - - - -
395A TRP* 5.8 1.3 - + - -
402A PRO* 3.2 4.1 - - + -
403A SER* 1.3 73.2 - - - +
405A GLY* 1.3 57.9 + - - +
424A VAL* 3.6 24.2 - - + -
425A GLY 3.6 5.2 - - - -
426A ALA* 3.8 17.5 - - + -
433A ILE* 3.7 30.7 - - + -
435A TYR* 3.6 26.7 - + - -
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Residues in contact with GLY 405 (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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343A ALA* 3.4 8.8 - - - +
361A ALA* 3.0 33.7 - - - +
363A PRO* 4.0 2.8 - - - +
373A VAL* 4.0 5.4 - - - -
404A PHE* 1.3 72.3 - - - +
406A TYR* 1.3 64.0 + - - +
407A SER 3.0 4.7 + - - -
408A MET* 3.9 2.9 - - - +
424A VAL* 3.4 22.8 - - - +
425A GLY 3.0 8.5 + - - -
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Residues in contact with TYR 406 (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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21A PHE* 3.4 33.7 - + - -
278A PHE* 3.6 22.9 - + - -
342A SER* 4.7 8.8 - - - +
343A ALA* 3.9 11.0 - - - +
363A PRO* 3.7 12.0 - - + +
364A TYR* 4.0 30.5 - + - -
403A SER* 3.1 20.8 + - - +
404A PHE 3.4 1.0 - - - -
405A GLY* 1.3 76.9 - - - +
407A SER* 1.3 58.6 + - - +
425A GLY 4.8 0.9 - - - +
427A PHE* 3.7 22.0 - + + -
258B LEU* 5.7 3.6 - - + +
261B ARG* 3.5 37.0 + - - -
266B VAL* 3.6 19.1 - - + +
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Residues in contact with SER 407 (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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20A GLY 2.7 25.9 + - - -
21A PHE 3.3 22.6 + - - -
22A ALA* 4.2 5.8 - - - -
23A VAL* 3.7 12.8 - - - +
343A ALA* 4.6 3.1 - - - -
405A GLY 4.0 1.1 - - - -
406A TYR* 1.3 79.8 - - - +
408A MET* 1.3 68.7 + - - +
425A GLY* 2.8 31.9 + - - +
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Residues in contact with MET 408 (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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23A VAL* 3.6 9.4 - - - +
343A ALA* 3.2 31.1 - - + +
345A ALA* 3.4 25.3 - - + +
359A ALA* 3.1 33.0 - - - +
361A ALA* 3.9 10.1 - - + -
373A VAL* 3.5 31.9 - - - -
405A GLY* 3.9 10.8 - - - +
407A SER* 1.3 83.8 - - - +
409A LYS* 1.3 68.2 + - - +
422A LEU* 4.3 4.5 - - + -
423A ILE 3.2 12.8 - - - +
424A VAL* 4.4 7.6 - - + -
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Residues in contact with LYS 409 (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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23A VAL* 3.7 18.3 - - + +
24A ASP* 2.8 50.4 + - - +
25A PHE* 3.4 20.6 - - + +
99A ARG* 3.0 32.4 - - - +
345A ALA* 4.6 3.1 - - + -
346A PRO 5.9 0.4 - - - +
408A MET* 1.3 79.1 - - - +
410A GLY* 1.3 70.6 + - - +
411A ALA* 6.1 1.2 - - + +
412A THR* 5.4 1.4 + - - -
422A LEU* 3.1 6.0 - - - +
423A ILE* 2.7 38.8 + - + -
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Residues in contact with GLY 410 (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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25A PHE* 3.3 15.0 - - - -
345A ALA* 4.9 1.4 - - - +
346A PRO 3.8 14.0 + - - -
347A LEU* 4.3 4.0 - - - +
409A LYS* 1.3 84.7 + - - +
411A ALA* 1.3 72.2 + - - +
412A THR* 3.1 7.2 + - - -
421A ASP 3.3 15.3 - - - -
422A LEU* 4.1 7.1 - - - +
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Residues in contact with ALA 411 (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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346A PRO* 4.0 12.8 - - + +
347A LEU 3.3 30.7 + - - -
348A GLY* 4.2 6.1 - - - +
409A LYS* 6.1 1.3 - - + +
410A GLY* 1.3 72.2 - - - +
412A THR* 1.3 61.0 + - - +
413A ASP 4.3 0.4 + - - -
420A PRO* 4.1 6.9 - - - +
421A ASP 3.8 3.0 + - - -
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Residues in contact with THR 412 (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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25A PHE* 3.5 51.7 - - + +
27A VAL* 3.8 10.0 - - + +
34A MET* 3.4 32.5 - - + -
409A LYS* 5.4 1.9 + - - -
410A GLY 3.1 3.9 + - - -
411A ALA* 1.3 81.5 + - - +
413A ASP* 1.3 60.5 + - - +
414A ILE* 2.8 10.4 + - - +
420A PRO* 4.0 2.4 - - - +
421A ASP* 3.3 15.7 + - - +
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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