Contacts of the helix formed by residues 385 - 396 (chain B) in PDB entry 2P1N
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 THR 385 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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361B GLU* 4.0 6.1 + - - +
384B MET* 1.3 86.0 - - - +
386B ASN* 1.3 64.9 + - - +
387B ALA* 3.6 11.1 - - - +
388B ALA* 2.8 30.5 + - - +
389B LEU* 3.1 26.3 + - - +
413B ASP* 3.3 23.3 - - - +
414B TYR* 3.5 22.9 - - + -
415B LEU* 3.6 17.9 - - + +
420B LEU* 3.7 7.2 - - - -
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Residues in contact with ASN 386 (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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385B THR* 1.3 70.6 - - - +
387B ALA* 1.3 62.8 + - - +
389B LEU* 3.2 2.9 + - - +
390B ILE* 3.0 30.5 + - + +
413B ASP* 2.8 22.6 + - - +
416B THR* 4.7 2.5 - - + +
418B GLU* 4.2 7.9 - - - +
419B PRO 2.8 25.1 + - - -
420B LEU* 3.1 20.9 - - - +
422B ILE* 3.7 31.1 - - + +
423B GLY* 2.9 23.4 + - - -
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Residues in contact with ALA 387 (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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385B THR* 3.2 9.3 + - - +
386B ASN* 1.3 78.6 - - - +
388B ALA* 1.3 63.3 + - - +
390B ILE* 3.2 18.7 + - - +
391B THR* 3.2 18.0 + - - +
413B ASP* 4.4 0.8 + - - -
415B LEU* 6.1 2.9 - - + -
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Residues in contact with ALA 388 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
361B GLU* 3.5 28.5 - - + +
365B VAL* 3.7 19.5 - - + -
384B MET* 4.1 5.6 - - - -
385B THR* 2.8 26.1 + - - +
387B ALA* 1.3 74.4 - - - +
389B LEU* 1.3 63.9 + - - +
391B THR* 3.1 4.8 + - - -
392B ILE* 3.0 31.6 + - + +
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Residues in contact with LEU 389 (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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384B MET* 3.9 25.8 - - + -
385B THR 3.1 17.2 + - - +
386B ASN 3.2 0.6 + - - +
388B ALA* 1.3 77.2 - - - +
390B ILE* 1.3 59.1 + - - +
392B ILE* 3.1 10.6 + - + +
393B ALA* 2.9 29.8 + - - +
402B PHE* 4.3 22.4 - - + -
404B LEU* 4.3 15.0 - - + -
420B LEU* 4.6 5.6 - - + -
423B GLY* 3.4 40.8 - - - +
424B PHE* 3.9 24.9 - - + +
427B ILE* 3.9 6.4 - - + +
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Residues in contact with ILE 390 (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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386B ASN* 3.0 25.2 + - + +
387B ALA* 3.6 9.0 - - - +
388B ALA 3.1 0.2 - - - -
389B LEU* 1.3 79.5 - - - +
391B THR* 1.3 56.0 + - - +
393B ALA* 4.0 1.0 - - - +
394B ARG* 3.2 56.0 + - - +
422B ILE* 4.3 23.3 - - + +
423B GLY* 4.4 0.7 - - - -
426B ALA* 4.0 25.5 - - + +
430B HIS* 5.5 0.4 - - + -
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Residues in contact with THR 391 (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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365B VAL* 3.7 25.1 - - + -
369B MET* 3.9 12.6 - - + -
387B ALA* 3.2 12.9 + - - +
388B ALA* 3.1 9.8 + - - -
389B LEU 3.1 0.6 - - - -
390B ILE* 1.3 75.1 - - - +
392B ILE* 1.3 61.7 + - - +
394B ARG* 3.7 7.7 - - - +
395B ASN* 2.8 53.8 + - - +
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Residues in contact with ILE 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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361B GLU 5.0 0.2 - - - +
364B LEU* 3.5 37.0 - - + -
365B VAL* 4.2 14.4 - - + -
368B SER* 3.1 28.0 - - - +
384B MET* 5.3 2.5 - - - -
388B ALA* 3.0 24.3 + - + +
389B LEU* 3.4 19.5 - - + +
391B THR* 1.3 79.2 - - - +
393B ALA* 1.3 63.3 + - - +
395B ASN* 3.1 1.0 + - - -
396B ARG* 3.0 26.0 + - - +
399B MET* 4.3 10.5 - - + -
402B PHE* 4.0 25.1 - - + -
427B ILE* 4.2 5.2 - - + -
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Residues in contact with ALA 393 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
389B LEU 2.9 14.7 + - - +
390B ILE 4.0 3.6 - - - +
392B ILE* 1.3 76.4 - - - +
394B ARG* 1.3 68.1 + - - +
395B ASN 3.1 0.7 + - - -
396B ARG 3.4 6.4 + - - -
397B PRO* 3.6 14.2 - - - +
426B ALA* 3.2 39.0 - - + +
427B ILE* 3.6 15.9 - - - +
430B HIS* 4.1 14.1 - - + +
431B CYS* 4.4 7.0 - - - -
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Residues in contact with ARG 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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390B ILE* 3.2 38.0 + - - +
391B THR* 3.7 8.7 - - - +
393B ALA* 1.3 79.8 - - - +
395B ASN* 1.3 64.4 + - - +
396B ARG 3.5 0.2 + - - -
397B PRO* 3.6 9.2 - - - +
426B ALA* 6.1 0.4 - - - +
430B HIS* 3.7 33.5 + - + -
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Residues in contact with ASN 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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368B SER* 3.3 24.6 - - - +
369B MET* 2.7 50.7 - - - +
391B THR* 2.8 41.5 + - - +
392B ILE 3.1 2.1 + - - +
394B ARG* 1.3 79.9 - - - +
396B ARG* 1.4 89.7 + - + +
397B PRO* 3.3 4.7 - - - +
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Residues in contact with ARG 396 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
368B SER* 3.0 38.0 + - - +
369B MET* 4.5 6.5 + - - +
371B CYS 3.9 10.4 + - - -
372B PRO* 3.1 41.9 + - - +
374B LEU* 3.6 23.3 - - - +
392B ILE 3.0 13.4 + - - +
393B ALA 3.8 3.8 - - - -
394B ARG 3.3 0.2 - - - -
395B ASN* 1.4 104.5 + - + +
397B PRO* 1.3 62.7 - - - +
398B ASN* 2.8 34.1 + - - +
399B MET* 2.9 36.3 + - + +
431B CYS* 3.7 5.5 - - - -
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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