Contacts of the helix formed by residues 360 - 371 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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327E ASP* 2.6 30.3 + - - +
357E VAL 5.4 0.4 - - - +
358E ALA* 4.2 4.5 - - - -
359E LEU* 1.3 88.0 - - - +
361E GLU* 1.3 81.4 + - - +
362E GLN* 2.9 7.8 + - - +
379E TYR* 2.7 31.7 + - - -
381E CYS* 4.7 3.4 - - - -
383E GLN* 3.6 26.4 + - + +
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Residues in contact with GLU 361 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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360E THR* 1.3 86.2 + - - +
362E GLN* 1.3 64.6 + - - +
364E LEU* 3.2 6.7 + - - +
365E VAL* 3.1 20.9 + - + +
379E TYR* 5.1 0.9 - - - -
383E GLN* 3.0 22.6 + - - +
384E MET* 3.8 38.4 - - - -
385E THR* 3.9 14.2 + - + +
388E ALA* 3.5 24.4 - - + +
392E ILE* 5.1 0.7 - - + +
414E TYR* 3.1 27.6 + - - -
415E LEU* 5.5 1.4 - - - +
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Residues in contact with GLN 362 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327E ASP* 3.4 22.0 - - + +
360E THR* 2.9 8.5 + - - +
361E GLU* 1.3 79.9 + - + +
363E GLY* 1.3 55.5 + - - +
364E LEU 3.2 0.2 + - - -
365E VAL* 3.3 26.4 + - - +
366E SER* 2.8 48.6 + - - +
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Residues in contact with GLY 363 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327E ASP* 3.0 25.9 + - - +
330E LEU* 3.4 36.0 - - - +
360E THR 3.6 0.2 + - - -
361E GLU 3.5 0.2 - - - -
362E GLN* 1.3 73.6 - - - +
364E LEU* 1.3 62.4 + - - +
366E SER* 3.2 7.0 + - - -
367E VAL* 3.1 23.9 + - - +
379E TYR* 3.7 1.8 - - - -
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Residues in contact with LEU 364 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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343E LEU* 5.0 3.1 - - + -
361E GLU* 3.2 8.7 + - - +
362E GLN 3.2 0.8 - - - -
363E GLY* 1.3 72.1 - - - +
365E VAL* 1.3 61.5 + - - +
367E VAL* 3.2 7.2 + - + -
368E SER* 2.8 30.3 + - - +
374E LEU* 4.8 8.3 - - + -
377E VAL* 4.0 28.7 - - + -
379E TYR* 3.5 40.0 + - + -
384E MET* 5.1 2.0 - - + -
392E ILE* 3.4 26.7 - - + -
399E MET* 5.8 0.2 - - + -
402E PHE* 4.1 11.9 - - + -
404E LEU* 3.6 31.0 - - + -
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Residues in contact with VAL 365 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
361E GLU* 3.1 17.2 + - + +
362E GLN* 3.4 28.3 - - - +
364E LEU* 1.3 73.9 - - - +
366E SER* 1.3 66.5 + - - +
368E SER* 2.8 23.5 - - - -
369E MET* 3.1 28.7 + - + +
388E ALA* 3.5 38.6 - - + +
391E THR* 4.1 12.6 - - + -
392E ILE* 4.0 4.7 - - + +
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Residues in contact with SER 366 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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327E ASP 5.2 1.0 + - - -
330E LEU 4.5 1.1 - - - -
331E GLU* 4.0 35.0 - - - +
334E ALA* 3.6 9.7 - - - +
362E GLN* 2.8 33.9 + - - +
363E GLY* 3.4 10.6 - - - -
365E VAL* 1.3 72.7 - - - +
367E VAL* 1.3 59.0 + - - +
369E MET* 2.9 10.4 + - - +
370E GLY* 2.8 24.8 + - - -
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Residues in contact with VAL 367 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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330E LEU* 3.5 31.0 - - + +
333E LEU* 3.5 25.8 - - + -
334E ALA* 3.8 10.8 - - + -
340E LEU* 5.0 1.1 - - + -
343E LEU* 3.8 18.6 - - + -
363E GLY 3.1 13.2 + - - +
364E LEU* 3.9 4.5 - - + +
366E SER* 1.3 79.7 - - - +
368E SER* 1.3 62.8 + - - +
371E CYS* 3.0 31.1 + - - +
374E LEU* 3.4 28.1 - - + +
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Residues in contact with SER 368 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364E LEU* 2.8 13.1 + - - +
365E VAL* 2.8 20.2 - - - -
367E VAL* 1.3 79.7 - - - +
369E MET* 1.3 55.7 + - - -
374E LEU* 4.4 6.0 - - - +
392E ILE* 3.2 39.4 + - - +
395E ASN* 3.6 15.1 - - - +
396E ARG* 3.0 40.5 + - - +
399E MET* 5.2 0.7 - - - +
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Residues in contact with MET 369 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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365E VAL* 3.2 24.5 - - - +
366E SER* 2.9 7.8 + - - +
368E SER* 1.3 79.4 - - - +
370E GLY* 1.3 62.5 + - - +
371E CYS 3.4 1.1 + - - -
372E PRO* 5.5 0.3 - - - +
391E THR* 4.1 15.3 - - + -
395E ASN* 3.1 35.2 - - - +
396E ARG* 4.6 5.0 + - - +
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Residues in contact with GLY 370 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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334E ALA* 3.3 16.2 - - - +
338E LYS* 2.5 30.9 + - - -
366E SER 2.8 14.5 + - - -
369E MET* 1.3 80.6 - - - +
371E CYS* 1.3 63.0 + - - +
372E PRO* 3.4 8.7 - - - +
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Residues in contact with CYS 371 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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333E LEU 4.6 1.3 - - - -
334E ALA* 3.8 21.8 - - - -
337E CYS 3.8 20.2 - - - +
338E LYS 5.1 0.2 - - - -
340E LEU* 4.3 19.5 - - + +
367E VAL* 3.0 28.3 + - - +
368E SER 4.2 0.2 - - - -
369E MET 3.4 2.0 - - - -
370E GLY* 1.3 85.6 - - - +
372E PRO* 1.3 67.8 - - - +
373E LYS 2.9 3.9 + - - -
374E LEU* 3.1 24.7 + - + +
396E ARG* 3.4 14.9 + - - -
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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