Contacts of the helix formed by residues 391 - 402 (chain B) in PDB entry 2P20
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 ASN 391 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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362B ARG* 5.0 9.0 - - - +
389B PRO* 4.1 1.4 + - - +
390B ILE* 1.3 76.0 - - - +
392B PRO* 1.3 75.2 - - + +
393B GLU* 3.6 32.5 + - - +
394B ALA* 3.1 20.8 + - - +
395B TRP* 3.0 18.1 + - - -
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Residues in contact with PRO 392 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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390B ILE 3.8 2.4 - - - +
391B ASN* 1.3 89.4 - - + +
393B GLU* 1.3 56.1 + - + +
395B TRP* 3.3 3.4 + - + +
396B GLU* 2.8 41.4 + - + +
434B ALA* 3.8 33.7 - - + +
435B GLY* 4.9 1.3 - - - -
511B TRP* 5.2 5.8 - - + -
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Residues in contact with GLU 393 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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573A PRO* 3.3 41.2 - - + +
365B MET* 3.6 7.3 - - + +
391B ASN* 3.2 18.6 + - - +
392B PRO* 1.3 76.0 - - + +
394B ALA* 1.3 60.6 + - - +
396B GLU* 4.0 5.8 - - - +
397B TRP* 3.1 28.6 + - - +
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Residues in contact with ALA 394 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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358B PRO* 5.9 0.7 - - + +
361B ILE* 3.8 12.0 - - + +
362B ARG* 4.6 13.9 - - + -
365B MET* 3.8 19.0 - - - +
390B ILE* 3.9 16.2 - - + -
391B ASN* 3.1 25.2 + - - +
393B GLU* 1.3 75.3 - - - +
395B TRP* 1.3 61.1 + - - +
397B TRP* 3.3 2.6 + - - +
398B TYR* 2.9 30.3 + - - +
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Residues in contact with TRP 395 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7B HIS* 3.6 38.4 - + - -
385B SER* 5.8 0.4 - - - -
390B ILE* 3.7 29.0 - - + +
391B ASN 3.0 12.1 + - - +
392B PRO* 3.4 10.3 - - + +
394B ALA* 1.3 75.5 - - - +
396B GLU* 1.3 62.4 + - - +
398B TYR* 3.3 6.7 + - - +
399B TRP* 2.9 58.3 + + + +
409B VAL* 3.5 40.3 + - + +
411B ASP* 4.7 9.2 - - + +
432B LEU* 3.7 28.0 - - + -
433B LYS 4.5 2.4 + - - -
434B ALA* 3.6 25.6 - - + -
435B GLY 3.5 17.2 - - - +
436B SER 5.3 1.0 + - - -
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Residues in contact with GLU 396 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7B HIS* 3.0 35.1 + - - -
392B PRO* 2.8 26.3 + - + +
393B GLU* 4.0 6.1 - - - +
395B TRP* 1.3 78.1 - - - +
397B TRP* 1.3 52.2 - - - +
399B TRP* 3.4 13.1 + - - +
400B LYS* 2.8 37.4 + - - +
434B ALA* 3.6 17.1 - - + +
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Residues in contact with TRP 397 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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574A GLU* 4.8 19.3 - - + +
361B ILE* 4.1 14.6 - - + -
364B LEU* 3.8 6.5 - - + -
365B MET* 3.7 60.1 + - + +
368B GLY* 3.5 27.6 - - - -
371B ALA* 3.7 21.5 - - + -
372B ILE* 5.2 1.8 - - + -
393B GLU 3.1 19.2 + - - +
394B ALA 3.5 4.3 - - - +
396B GLU* 1.3 72.2 - - - +
398B TYR* 1.3 66.1 + + - +
400B LYS* 4.7 4.0 - - - -
401B LYS* 2.7 72.8 + - + +
402B ILE* 4.0 26.9 - - + -
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Residues in contact with TYR 398 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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342B MET* 5.1 2.2 - - + -
354B LEU* 3.5 21.1 + - + +
356B THR* 3.5 15.3 - - + +
361B ILE* 3.5 41.1 - - + -
383B LEU* 3.5 22.6 - - + +
384B GLY 2.9 32.8 + - - -
385B SER* 4.6 0.7 - - - -
390B ILE* 5.0 4.0 - - + -
394B ALA 2.9 12.9 + - - +
395B TRP* 3.4 9.9 - - - +
397B TRP* 1.3 83.2 - + - +
399B TRP* 1.3 62.1 + - - +
402B ILE* 3.1 53.4 + - + +
403B GLY 3.2 7.3 + - - -
409B VAL* 4.2 22.2 - - + -
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Residues in contact with TRP 399 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7B HIS* 3.5 35.7 + + + +
383B LEU* 4.3 6.3 - - - -
395B TRP* 2.9 45.9 + + + +
396B GLU* 3.5 18.4 - - - +
397B TRP 3.2 0.2 - - - -
398B TYR* 1.3 78.1 - - - +
400B LYS* 1.3 62.7 + - + +
403B GLY* 3.4 5.5 - - - -
404B LYS 3.3 5.9 + - - -
405B GLU* 3.0 72.1 + - + -
406B LYS 5.7 0.2 - - - -
407B CYS 3.2 31.8 + - - +
408B PRO* 4.8 2.6 - - - +
409B VAL* 3.8 8.1 - - + -
432B LEU* 5.2 1.0 - - - +
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Residues in contact with LYS 400 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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574A GLU* 4.1 27.2 + - - +
377B ARG* 5.4 0.2 + - - -
396B GLU 2.8 21.6 + - - +
397B TRP* 4.0 2.9 - - - +
399B TRP* 1.3 78.1 - - + +
401B LYS* 1.3 74.7 + - + +
404B LYS* 3.0 27.5 + - - +
405B GLU* 3.5 35.6 - - + +
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Residues in contact with LYS 401 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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574A GLU* 3.2 37.8 + - - -
369B ASP* 2.9 34.7 + - - +
372B ILE* 3.5 22.1 - - + +
377B ARG* 3.1 30.7 + - - +
397B TRP* 2.7 62.9 + - + +
400B LYS* 1.3 89.5 - - + +
402B ILE* 1.3 60.9 + - - +
404B LYS 4.4 0.3 + - - -
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Residues in contact with ILE 402 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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342B MET* 4.1 14.1 - - + -
343B CYS* 3.6 28.3 - - - -
354B LEU* 3.9 21.5 - - + -
364B LEU* 5.0 2.9 - - + -
371B ALA* 5.1 1.1 - - + +
372B ILE* 3.9 14.4 - - + -
377B ARG* 3.8 16.3 - - - +
380B LEU* 3.4 31.9 - - + +
383B LEU* 4.1 3.1 - - + -
397B TRP* 4.0 24.0 - - + -
398B TYR* 3.1 36.2 + - + +
401B LYS* 1.3 78.2 - - - +
403B GLY* 1.3 60.8 + - - +
404B LYS* 3.4 0.6 + - - +
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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