Contacts of the helix formed by residues 327 - 338 (chain A) in PDB entry 1N35
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 327 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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279A GLN* 2.9 55.7 + - - +
283A HIS* 3.6 15.4 + - - +
284A SER* 3.0 9.5 + - - -
287A GLU* 5.6 0.7 - - - +
322A ARG* 4.0 8.8 + - - +
325A PRO 3.7 1.2 + - - +
326A SER* 1.3 73.0 - - - +
328A ASP* 1.3 66.5 + - - +
329A LYS 3.2 3.8 + - - -
330A LYS* 3.3 12.3 + - + +
331A ALA* 2.9 22.5 + - - +
348A ARG* 2.8 24.5 + - - +
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Residues in contact with ASP 328 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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287A GLU* 5.6 0.2 - - - +
326A SER* 3.4 17.5 + - - +
327A ASN* 1.3 75.8 - - - +
329A LYS* 1.3 63.3 + - - +
331A ALA* 3.6 0.9 - - - +
332A ARG* 2.7 69.2 + - - +
348A ARG* 3.4 27.5 + - - +
352A LYS* 4.9 3.3 + - - +
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Residues in contact with LYS 329 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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326A SER 5.1 1.9 + - - +
327A ASN 3.3 0.8 - - - -
328A ASP* 1.3 86.2 + - - +
330A LYS* 1.3 60.9 + - + +
332A ARG* 3.3 4.5 + - - +
333A GLU* 2.9 57.1 + - + +
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Residues in contact with LYS 330 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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279A GLN* 6.0 1.1 - - - +
327A ASN* 3.3 13.8 + - + +
329A LYS* 1.3 80.2 - - + +
331A ALA* 1.3 58.0 + - - +
333A GLU* 3.2 15.1 + - - +
334A LEU* 2.9 31.4 + - - +
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Residues in contact with ALA 331 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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279A GLN* 4.8 9.6 + - + +
280A ASN* 3.5 27.8 + - - +
327A ASN* 2.9 23.8 + - - +
328A ASP 3.6 2.0 - - - +
330A LYS* 1.3 77.0 - - - +
332A ARG* 1.3 56.6 + - - +
334A LEU* 3.4 9.7 + - - +
335A GLY 3.1 21.0 + - - -
344A VAL* 3.8 12.1 - - + +
348A ARG* 3.6 13.2 - - - +
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Residues in contact with ARG 332 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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328A ASP* 2.7 48.8 + - - +
329A LYS* 3.8 4.0 - - - +
331A ALA* 1.3 72.2 - - - +
333A GLU* 1.3 66.1 + - + +
335A GLY* 3.4 1.0 + - - +
336A GLU* 3.0 31.6 + - + +
341A SER* 5.1 2.6 + - - -
344A VAL* 4.2 15.0 - - + +
345A GLY* 4.0 21.2 + - - +
348A ARG* 3.6 29.0 - - - +
352A LYS* 4.9 6.1 - - - +
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Residues in contact with GLU 333 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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329A LYS* 2.9 51.7 + - + +
330A LYS* 3.2 15.8 + - - +
332A ARG* 1.3 76.5 - - + +
334A LEU* 1.3 58.9 + - - +
336A GLU* 3.3 7.9 + - - +
337A LYS* 2.9 30.5 + - - +
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Residues in contact with LEU 334 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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272A LYS 4.1 17.5 - - - +
273A THR* 4.5 2.7 - - + -
275A SER* 3.7 21.5 - - - +
276A ILE* 3.8 31.2 - - + -
279A GLN* 6.2 0.2 - - + -
330A LYS 2.9 13.1 + - - +
331A ALA* 3.5 12.6 - - - +
332A ARG 3.2 0.2 - - - -
333A GLU* 1.3 78.0 - - - +
335A GLY* 1.3 62.2 + - - +
337A LYS* 3.3 4.6 + - - -
338A TYR* 3.2 41.6 + - + +
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Residues in contact with GLY 335 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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331A ALA 3.1 10.9 + - - -
332A ARG 3.4 2.7 + - - -
333A GLU 3.3 0.4 - - - -
334A LEU* 1.3 80.5 - - - +
336A GLU* 1.3 60.8 + - - +
338A TYR* 3.3 1.8 + - - -
339A GLY 3.2 3.5 + - - -
340A LEU* 2.7 32.1 + - - -
341A SER* 3.2 11.8 + - - -
344A VAL* 3.8 24.7 - - - -
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Residues in contact with GLU 336 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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332A ARG* 3.0 25.0 + - + +
333A GLU* 3.5 7.4 - - - +
335A GLY* 1.3 75.6 - - - +
337A LYS* 1.3 62.5 + - - +
338A TYR 3.4 0.5 + - - -
339A GLY* 3.5 9.3 + - - +
341A SER* 3.6 25.9 + - - -
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Residues in contact with LYS 337 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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333A GLU 2.9 17.4 + - - +
334A LEU* 3.7 6.7 - - - +
335A GLY 3.3 0.2 - - - -
336A GLU* 1.3 78.5 - - - +
338A TYR* 1.3 90.8 + - + +
339A GLY 3.5 0.7 + - - -
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Residues in contact with TYR 338 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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259A HIS* 4.3 2.3 - - - -
268A TRP* 3.8 23.0 - + - -
269A PHE* 3.3 41.1 - + + -
272A LYS* 3.1 48.8 + - + +
273A THR* 3.6 29.8 - - + -
334A LEU* 3.2 35.6 + - + +
335A GLY 3.3 0.4 + - - +
336A GLU 3.3 0.2 - - - -
337A LYS* 1.3 111.4 + - + +
339A GLY* 1.3 63.5 + - - +
340A LEU* 3.3 7.1 - - + +
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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