Contacts of the helix formed by residues 377 - 386 (chain D) in PDB entry 2NPP
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 CYS 377 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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339D GLN* 4.0 43.7 - - + +
342D LYS* 5.2 2.4 - - - +
343D SER* 4.7 2.0 - - - -
375D ASP* 3.0 12.7 + - - +
376D GLU* 1.3 77.0 - - - +
378D PRO* 1.3 74.2 - - - +
379D GLU* 3.2 35.7 - - - -
380D VAL* 2.8 30.6 + - + +
381D ARG* 3.3 5.4 + - - +
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Residues in contact with PRO 378 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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339D GLN* 5.7 1.3 - - - +
376D GLU 3.0 5.6 - - - +
377D CYS* 1.3 82.5 - - + +
379D GLU* 1.3 73.1 + - - +
380D VAL 2.8 0.7 + - - -
381D ARG* 2.9 29.9 + - - +
382D LEU* 2.6 37.4 + - + +
416D LYS* 3.7 32.8 - - + +
419D VAL* 4.3 9.8 - - + +
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Residues in contact with GLU 379 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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339D GLN* 5.5 1.8 - - - +
343D SER* 3.6 20.0 - - - +
377D CYS* 3.2 18.7 - - - -
378D PRO* 1.3 89.0 - - - +
380D VAL* 1.3 56.4 + - - +
382D LEU* 4.1 9.5 - - - +
383D ASN* 2.7 41.1 + - - +
293F PRO* 6.0 2.3 - - - +
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Residues in contact with VAL 380 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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339D GLN 4.5 0.2 - - - +
342D LYS* 3.7 15.0 - - + +
343D SER* 3.3 32.3 - - - +
346D ALA* 3.9 13.2 - - + +
372D GLN* 3.8 24.2 - - + +
375D ASP* 3.5 25.8 - - + +
377D CYS* 2.8 26.6 + - + +
379D GLU* 1.3 74.8 - - - +
381D ARG* 1.3 66.6 + - - +
383D ASN* 3.1 3.1 + - - +
384D ILE* 2.9 21.5 + - - +
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Residues in contact with ARG 381 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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372D GLN 3.4 22.0 - - - +
373D LEU* 3.7 18.2 - - - +
374D LYS* 4.4 1.1 - - - +
375D ASP 3.1 26.9 + - - +
376D GLU* 3.1 20.3 + - - -
377D CYS 4.1 1.8 - - - +
378D PRO* 2.9 29.1 + - + +
380D VAL* 1.3 74.4 - - - +
382D LEU* 1.3 64.9 + - - +
384D ILE* 2.9 12.6 + - - +
385D ILE* 2.9 22.9 + - + +
411D LEU* 4.2 11.2 - - + +
414D ASP* 2.3 46.0 + - - +
415D ALA* 5.0 2.2 - - - +
416D LYS* 4.4 5.7 - - - +
419D VAL* 4.5 6.9 - - + +
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Residues in contact with LEU 382 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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378D PRO* 2.6 24.1 + - + +
379D GLU* 3.7 7.6 - - - +
381D ARG* 1.3 74.0 - - - +
383D ASN* 1.3 69.7 + - - +
384D ILE 3.3 0.2 + - - -
385D ILE* 3.6 8.1 + - - +
386D SER* 2.9 25.0 + - - +
418D ARG* 3.1 49.1 - - + +
419D VAL* 3.8 12.9 - - + +
422D ALA* 4.6 9.2 - - + +
295F ARG* 5.1 11.9 - - - +
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Residues in contact with ASN 383 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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343D SER* 3.4 22.2 + - - +
344D ALA* 5.4 0.2 - - - +
346D ALA* 3.4 19.1 - - + +
347D SER* 3.6 18.6 - - - +
379D GLU* 2.7 32.8 + - - +
380D VAL 3.1 3.8 + - - +
382D LEU* 1.3 88.4 - - - +
384D ILE* 1.3 58.3 + - - +
386D SER* 2.8 7.0 + - - -
387D ASN* 2.7 27.0 + - - -
295F ARG* 5.7 1.9 + - - -
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Residues in contact with ILE 384 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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346D ALA* 3.9 9.8 + - + +
349D ILE* 4.9 1.3 - - + -
350D MET* 4.4 10.5 - - + -
369D PHE* 4.2 17.5 - - + +
372D GLN* 3.3 35.9 - - + +
373D LEU* 3.1 52.5 - - + -
380D VAL 2.9 13.1 + - - +
381D ARG 2.9 10.0 + - - +
383D ASN* 1.3 75.7 - - - +
385D ILE* 1.3 72.5 + - - +
387D ASN* 3.0 15.5 + - + +
388D LEU* 3.9 14.3 - - + +
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Residues in contact with ILE 385 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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373D LEU* 3.2 28.3 - - + -
381D ARG 2.9 20.0 - - - +
382D LEU* 3.7 8.7 - - - +
384D ILE* 1.3 82.2 - - - +
386D SER* 1.3 58.2 + - - +
387D ASN 2.8 6.8 + - - -
388D LEU* 3.0 26.8 + - + +
389D ASP* 4.5 2.8 - - - +
408D ILE* 5.8 0.4 - - + -
411D LEU* 3.7 16.8 - - + -
419D VAL* 5.0 4.9 - - + -
422D ALA* 3.9 28.0 - - + +
423D ILE* 3.4 38.6 - - + -
426D TYR* 4.8 11.4 - - + +
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Residues in contact with SER 386 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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382D LEU* 2.9 12.5 + - - +
383D ASN* 2.8 23.9 + - - -
385D ILE* 1.3 74.3 - - - +
387D ASN* 1.3 64.5 + - - +
388D LEU 3.6 0.4 - - - -
389D ASP* 4.0 15.5 - - - +
422D ALA* 5.2 5.8 - - - +
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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