Contacts of the helix formed by residues 360 - 371 (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 360 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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327B ASP* 2.7 28.9 + - - +
358B ALA* 4.3 4.5 - - - -
359B LEU* 1.3 87.3 - - - +
361B GLU* 1.3 84.5 + - - +
362B GLN* 2.8 9.0 + - - +
363B GLY 3.3 2.8 + - - -
379B TYR* 2.8 23.0 + - - -
381B CYS* 4.5 4.9 - - - -
383B GLN* 3.7 28.3 - - - +
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Residues in contact with GLU 361 (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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360B THR* 1.3 89.5 + - - +
362B GLN* 1.3 68.5 + - - +
364B LEU* 3.3 7.6 + - - +
365B VAL* 3.1 22.3 + - + +
379B TYR* 5.1 0.2 - - - -
383B GLN* 3.4 9.9 + - - +
384B MET* 3.5 47.8 - - + -
385B THR* 4.0 6.7 + - - +
388B ALA* 3.5 24.9 - - + -
392B ILE* 5.0 0.3 - - - +
414B TYR* 2.9 31.5 + - + -
415B LEU* 5.2 1.2 - - - +
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Residues in contact with GLN 362 (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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327B ASP* 3.5 22.2 - - + +
331B GLU* 5.5 2.4 + - - -
360B THR* 2.8 7.5 + - - +
361B GLU* 1.3 86.1 + - - +
363B GLY* 1.3 63.4 + - - +
365B VAL* 3.2 21.7 + - - +
366B SER* 2.9 39.2 + - - +
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Residues in contact with GLY 363 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327B ASP* 3.2 26.7 + - - -
330B LEU* 3.6 31.5 - - - +
360B THR 3.3 2.0 + - - -
362B GLN* 1.3 72.7 - - - +
364B LEU* 1.3 62.3 + - - +
366B SER* 3.2 7.8 - - - -
367B VAL* 3.2 26.5 + - - +
379B TYR* 3.9 0.9 - - - -
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Residues in contact with LEU 364 (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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330B LEU* 4.9 0.2 - - - -
343B LEU* 4.9 8.5 - - + -
361B GLU* 3.3 9.7 + - - +
362B GLN 3.1 0.8 - - - -
363B GLY* 1.3 76.1 - - - +
365B VAL* 1.4 53.6 + - - +
367B VAL* 3.5 8.1 + - + +
368B SER* 2.8 37.4 + - - +
374B LEU* 5.0 2.5 - - + -
377B VAL* 4.0 29.2 - - + -
379B TYR* 3.5 46.9 + - + -
384B MET* 5.2 1.6 - - + -
392B ILE* 3.5 24.0 - - + -
399B MET* 5.8 0.4 - - + -
402B PHE* 4.0 22.7 - - + -
404B LEU* 4.4 8.3 - - + -
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Residues in contact with VAL 365 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
361B GLU 3.1 16.0 + - - +
362B GLN* 3.6 25.8 - - - +
364B LEU* 1.4 75.3 - - - +
366B SER* 1.3 69.0 + - - +
368B SER* 2.8 23.2 + - - -
369B MET* 3.1 19.8 + - - +
388B ALA* 3.7 36.8 - - + +
391B THR* 3.7 25.6 - - + -
392B ILE* 4.2 4.5 - - + +
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Residues in contact with SER 366 (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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327B ASP 4.7 1.0 + - - -
330B LEU 4.2 1.8 - - - -
331B GLU* 4.0 39.9 + - - +
334B ALA* 3.6 11.0 - - - +
362B GLN* 2.9 28.0 + - - +
363B GLY* 3.2 14.1 - - - -
365B VAL* 1.3 71.5 - - - +
367B VAL* 1.3 58.7 + - - +
369B MET* 2.9 22.6 + - - +
370B GLY* 3.0 10.4 + - - -
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Residues in contact with VAL 367 (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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330B LEU* 3.5 31.0 - - + +
333B LEU* 4.0 18.6 - - + -
334B ALA* 4.1 10.8 - - + +
340B LEU* 4.8 3.6 - - + -
343B LEU* 4.0 18.6 - - + -
363B GLY 3.2 13.8 + - - +
364B LEU* 3.7 5.8 - - + +
366B SER* 1.3 75.3 - - - +
368B SER* 1.3 65.8 + - - +
369B MET 3.2 0.3 + - - -
371B CYS* 3.3 31.6 + - - +
374B LEU* 3.3 27.1 - - + +
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Residues in contact with SER 368 (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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364B LEU* 2.8 17.7 + - - +
365B VAL* 2.8 16.8 + - - -
367B VAL* 1.3 75.6 - - - +
369B MET* 1.3 56.9 + - - +
374B LEU* 4.6 4.6 - - - +
392B ILE* 3.1 37.2 + - - +
395B ASN* 3.3 25.3 - - - +
396B ARG* 3.0 35.8 + - - +
399B MET* 5.4 0.3 - - - +
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Residues in contact with MET 369 (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* 3.3 20.4 - - + +
366B SER* 2.9 6.5 + - - +
368B SER* 1.3 79.8 - - - +
370B GLY* 1.3 61.3 + - - +
371B CYS 3.5 0.6 + - - -
372B PRO* 5.3 1.4 - - - +
391B THR* 3.9 16.8 - - + -
395B ASN* 2.7 47.8 - - - +
396B ARG* 4.5 5.4 + - - +
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Residues in contact with GLY 370 (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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334B ALA* 3.3 17.5 - - - +
338B LYS* 2.8 32.2 - - - +
366B SER 3.0 13.1 + - - -
367B VAL 3.5 0.2 + - - -
369B MET* 1.3 80.3 - - - +
371B CYS* 1.3 62.7 + - - +
372B PRO* 3.4 7.0 - - - +
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Residues in contact with CYS 371 (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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333B LEU 4.6 2.9 - - - -
334B ALA* 4.0 19.1 - - - -
337B CYS* 3.6 20.6 - - - +
338B LYS 4.6 3.6 - - - -
340B LEU* 4.2 20.4 - - + +
367B VAL* 3.3 28.3 + - - +
369B MET 3.5 1.6 - - - -
370B GLY* 1.3 81.7 - - - +
372B PRO* 1.3 56.4 - - - +
373B LYS 2.6 17.9 + - - -
374B LEU* 2.9 25.5 + - + +
396B ARG* 3.9 7.2 - - - -
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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