Contacts of the helix formed by residues 328 - 337 (chain B) in PDB entry 4NDH
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 SER 328 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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317B LEU* 3.4 10.3 - - - +
326B LEU* 3.3 3.2 + - - +
327B PRO* 1.3 82.9 - - - +
329B ILE* 1.3 59.4 + - - +
330B PRO* 3.4 7.1 - - - +
331B GLN* 3.2 31.6 + - - +
332B LEU* 2.8 28.9 + - - +
3H T 3.6 19.6 - - - -
4H C 3.4 13.7 - - - -
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Residues in contact with ILE 329 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273B LEU* 4.4 9.4 - - + +
274B LYS* 3.7 20.0 - - - +
275B ASN* 3.6 40.2 - - - +
276B LYS* 4.0 2.9 - - + +
279B TRP* 4.7 1.1 - - + -
317B LEU* 3.5 26.0 - - + +
328B SER* 1.3 68.0 - - - +
330B PRO* 1.4 66.8 - - + +
332B LEU* 3.1 12.2 + - + +
333B LYS* 2.8 51.8 + - + +
4H C 2.7 25.3 + - - +
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Residues in contact with PRO 330 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328B SER* 3.4 15.0 - - - +
329B ILE* 1.4 95.4 - - + +
331B GLN* 1.3 61.5 + - + +
333B LYS* 3.5 8.1 + - + +
334B GLU* 3.1 23.0 + - - +
3H T 3.8 42.0 - - - +
4H C 4.1 2.5 - - - +
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Residues in contact with GLN 331 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326B LEU* 4.0 10.4 - - + +
327B PRO* 3.3 40.0 - - + +
328B SER* 3.2 20.3 + - - +
329B ILE 3.2 0.4 - - - -
330B PRO* 1.3 76.3 - - + +
332B LEU* 1.3 61.6 + - - +
334B GLU* 3.4 7.5 + - - +
335B HIS* 2.9 29.1 + - - +
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Residues in contact with LEU 332 (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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273B LEU* 5.5 1.6 - - + -
279B TRP* 3.5 49.4 - - + +
317B LEU* 4.1 17.0 - - + -
318B ARG 4.9 0.9 - - - -
319B CYS* 4.5 9.9 - - + +
326B LEU* 3.9 30.9 - - + +
328B SER 2.8 21.1 + - - +
329B ILE* 3.1 15.0 + - + +
331B GLN* 1.3 73.6 - - - +
333B LYS* 1.3 60.0 + - + +
335B HIS* 2.9 4.2 + - + +
336B LEU* 2.9 54.8 + - + +
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Residues in contact with LYS 333 (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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268B PHE 5.0 4.0 + - - +
269B ASP* 5.9 0.4 - - - +
270B SER 2.8 33.5 + - - +
271B PRO* 4.4 5.2 - - - +
273B LEU* 2.9 27.9 + - + +
329B ILE* 2.8 42.8 + - + +
330B PRO* 3.9 7.4 - - + +
332B LEU* 1.3 77.6 - - + +
334B GLU* 1.3 59.4 + - - +
336B LEU* 3.7 17.9 + - + +
337B ARG* 3.4 24.1 + - - +
340B TRP* 5.0 3.5 - - - -
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Residues in contact with GLU 334 (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 PRO 3.1 16.7 + - - +
331B GLN* 3.6 8.5 - - - +
332B LEU 3.1 0.4 - - - -
333B LYS* 1.3 77.3 - - - +
335B HIS* 1.3 65.6 + - - +
337B ARG* 3.3 42.9 + - - +
338B LYS* 4.3 5.4 + - + +
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Residues in contact with HIS 335 (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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319B CYS* 3.5 17.7 - - + +
322B CYS* 3.4 4.9 - - - -
324B GLN* 3.1 39.3 + - + -
326B LEU* 3.9 17.9 - - + -
331B GLN 2.9 18.7 + - - +
332B LEU* 2.9 4.9 + - + +
334B GLU* 1.3 79.2 - - - +
336B LEU* 1.3 66.5 + - + +
338B LYS* 3.1 47.7 + - + +
339B HIS* 3.1 6.8 + + - -
402B ZN 2.0 37.3 - - - -
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Residues in contact with LEU 336 (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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267B ASP 4.2 4.5 - - - +
268B PHE* 4.2 19.1 - - + +
273B LEU* 5.2 2.0 - - + -
279B TRP* 3.7 31.9 - - + -
319B CYS* 4.1 17.7 - - - -
320B HIS* 3.8 27.8 - - + +
332B LEU* 2.9 32.4 + - + +
333B LYS* 4.0 13.2 - - + +
334B GLU 3.3 0.4 - - - -
335B HIS* 1.3 75.8 - - + +
337B ARG* 1.3 62.2 + - - +
339B HIS* 3.1 15.5 + - + +
340B TRP* 2.9 34.1 + - + +
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Residues in contact with ARG 337 (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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269B ASP* 5.6 1.2 + - - -
333B LYS* 3.4 21.2 + - - +
334B GLU* 3.3 37.7 + - - +
335B HIS 3.1 0.6 - - - -
336B LEU* 1.3 77.0 - - - +
338B LYS* 1.3 63.1 + - + +
340B TRP* 3.2 55.8 + - + +
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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