Contacts of the helix formed by residues 399 - 408 (chain M) in PDB entry 2PPB
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 399 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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397M GLU* 3.7 7.1 - - - -
398M THR* 1.3 79.5 - - - +
400M PRO* 1.3 77.7 - - + +
401M LEU* 3.3 17.8 + - - +
402M SER* 2.7 36.3 + - - -
403M SER 3.3 2.4 + - - -
565M GLN 3.6 2.8 + - - +
566M THR 3.4 11.9 + - - -
568M ALA 2.6 33.5 + - - +
569M VAL 4.9 0.2 - - - -
570M PRO* 3.7 11.4 - - + -
660M ALA* 5.2 2.0 - - + -
668M LEU* 3.2 29.6 - - + +
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Residues in contact with PRO 400 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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397M GLU* 5.3 0.9 - - + +
399M ASN* 1.3 84.0 - - + -
401M LEU* 1.3 64.9 + - - +
403M SER* 2.8 32.6 + - - +
404M LEU* 3.1 4.0 + - - +
570M PRO* 4.3 10.8 - - + -
587M VAL* 6.1 1.1 - - + -
588M VAL* 6.1 2.2 - - + -
591M SER* 4.7 9.8 - - - +
593M ALA* 4.2 22.2 - - + +
635M THR* 5.9 0.7 - - + -
637M LEU* 6.3 3.1 - - + -
659M PRO* 4.2 30.5 - - + -
660M ALA* 4.3 13.0 - - + +
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Residues in contact with LEU 401 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
399M ASN* 3.2 9.6 + - - +
400M PRO* 1.3 77.6 - - - +
402M SER* 1.3 64.8 + - - +
404M LEU* 3.5 12.8 + - + +
405M ARG* 3.0 24.1 + - + +
542M VAL* 5.1 2.5 - - + -
543M ASN* 4.4 13.7 - - + +
546M LEU* 4.2 23.1 - - + -
565M GLN* 3.8 36.1 - - + +
566M THR* 5.2 1.1 - - - -
587M VAL* 4.2 20.6 - - + +
666M LEU* 3.7 31.0 - - + -
668M LEU* 4.0 9.2 - - + -
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Residues in contact with SER 402 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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396M ASP* 2.5 46.5 + - - -
399M ASN* 2.7 44.2 + - - -
401M LEU* 1.3 75.6 - - - +
403M SER* 1.3 58.9 + - - -
405M ARG* 3.0 6.3 + - - +
406M HIS* 3.0 22.2 + - - +
566M THR* 3.3 22.6 - - - +
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Residues in contact with SER 403 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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395M LYS* 3.3 32.8 + - - +
396M ASP 3.2 11.9 + - - -
397M GLU* 3.8 12.8 - - - -
399M ASN 3.3 1.2 + - - -
400M PRO* 2.8 21.9 + - - +
402M SER* 1.3 73.5 - - - +
404M LEU* 1.3 81.4 + - - +
406M HIS* 3.0 6.5 + - - +
407M LYS* 3.0 28.4 + - - +
591M SER* 5.3 3.3 - - - -
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Residues in contact with LEU 404 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18M LEU* 3.3 40.2 - - + -
19M THR* 3.8 24.5 - - - +
400M PRO 3.1 5.7 + - - +
401M LEU* 3.5 14.1 - - + +
403M SER* 1.3 84.6 + - - +
405M ARG* 1.3 65.0 + - - +
407M LYS* 2.9 29.3 + - + +
408M ARG* 3.2 15.4 + - + +
542M VAL* 4.6 12.1 - - + -
587M VAL* 4.7 19.3 - - + +
591M SER* 4.5 17.7 - - - -
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Residues in contact with ARG 405 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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401M LEU* 3.0 16.3 + - + +
402M SER* 3.0 10.3 + - - +
404M LEU* 1.3 80.7 - - - +
406M HIS* 1.3 58.9 + - - +
407M LYS 3.0 1.4 + - - -
408M ARG* 3.0 9.6 + - + +
409M ARG* 2.9 45.6 + - - +
442M GLU* 3.0 39.9 + - - +
443M THR 6.2 0.2 - - - -
444M PRO* 5.7 1.2 - - - +
454M SER* 3.3 14.3 + - - +
543M ASN* 3.4 28.7 - - + +
563M ASN* 2.9 29.9 + - - +
566M THR* 3.4 29.6 + - + +
14Y G 3.4 26.9 + - - -
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Residues in contact with HIS 406 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135M VAL* 3.2 35.7 - - + +
137M VAL* 3.9 15.3 - - + +
393M GLN* 3.8 29.2 + - - +
394M PHE 3.5 24.0 + - - -
395M LYS* 4.0 1.4 - - - -
396M ASP* 4.0 28.5 - - + +
402M SER 3.0 11.5 + - - +
403M SER* 3.0 10.1 + - - +
405M ARG* 1.3 75.9 - - - +
407M LYS* 1.3 60.9 + - - +
409M ARG* 3.7 31.0 + - - +
13Y C 5.2 5.2 + - - -
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Residues in contact with LYS 407 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19M THR* 4.3 13.2 - - + -
22M GLN* 3.5 45.1 - - - +
124M ASP* 3.4 26.0 + - - +
125M GLY 3.8 5.4 - - - +
126M SER* 3.2 31.5 - - - +
135M VAL* 3.2 13.6 - - + +
136M ILE 4.4 3.3 - - - +
137M VAL* 5.0 1.4 - - - -
138M SER* 5.5 1.6 + - - -
395M LYS* 2.8 40.9 - - + +
403M SER* 3.0 14.5 + - - +
404M LEU* 2.9 20.7 + - + +
406M HIS* 1.3 82.3 - - - +
408M ARG* 1.3 58.4 + - + +
409M ARG 3.6 1.6 + - - +
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Residues in contact with ARG 408 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16M PRO* 6.2 0.6 - - - +
18M LEU* 3.2 49.8 + - - +
19M THR* 6.0 2.2 - - - -
21M ILE* 4.4 10.3 - - + -
22M GLN* 5.2 3.1 - - + -
138M SER* 5.1 5.0 + - - -
404M LEU* 3.7 16.2 - - + +
405M ARG* 3.0 17.4 + - - +
407M LYS* 1.3 80.6 - - + +
409M ARG* 1.3 63.7 + - - +
410M ILE* 3.4 3.6 + - - +
442M GLU* 5.8 0.4 - - - -
454M SER* 4.5 5.6 - - - -
455M LEU* 3.1 63.4 + - + +
456M ALA 2.8 25.7 + - - -
457M ALA 4.0 11.1 + - - -
542M VAL* 3.1 30.6 - - - +
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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