Contacts of the helix formed by residues 261 - 267 (chain A) in PDB entry 1NUA
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 GLY 261 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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262A GLY* 1.3 69.7 + - - +
263A LEU 3.8 0.4 - - - -
264A ARG* 4.5 29.4 - - - +
265A ASN* 3.3 22.5 + - - +
378A ARG* 5.2 5.7 + - - -
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Residues in contact with GLY 262 (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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261A GLY* 1.3 75.6 - - - +
263A LEU* 1.3 66.5 + - - +
265A ASN* 3.0 19.8 + - - +
266A LEU* 3.4 4.9 + - - +
377A THR* 3.1 28.3 - - - +
378A ARG* 4.6 6.3 - - - -
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Residues in contact with LEU 263 (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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249A HIS* 5.3 9.7 - - + +
252A TYR* 4.0 31.2 - - + -
253A VAL* 3.7 22.8 - - + +
256A ALA* 4.3 20.4 - - + -
262A GLY* 1.3 71.0 - - - +
264A ARG* 1.3 55.9 + - + +
266A LEU* 2.7 53.4 + - + +
267A LEU* 3.5 4.2 + - - +
377A THR* 4.0 1.2 + - - -
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Residues in contact with ARG 264 (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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253A VAL* 3.1 38.0 + - + +
254A VAL* 4.5 7.1 + - - +
256A ALA* 2.6 37.0 + - + +
261A GLY* 4.6 25.0 - - - +
262A GLY 3.4 0.6 - - - -
263A LEU* 1.3 76.5 - - + +
265A ASN* 1.3 56.9 + - - +
267A LEU* 2.9 28.4 + - + +
268A ASN* 4.1 6.9 + - - -
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Residues in contact with ASN 265 (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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261A GLY 3.3 13.3 + - - +
262A GLY 3.0 15.7 + - - +
264A ARG* 1.3 79.1 - - - +
266A LEU* 1.3 60.3 + - - +
267A LEU 3.0 0.2 - - - -
268A ASN* 3.1 29.1 + - - +
364A LYS* 4.1 7.3 + - - -
366A VAL* 3.2 16.1 - - - +
378A ARG* 4.5 7.6 + - - -
379A ALA* 3.2 38.9 + - - +
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Residues in contact with LEU 266 (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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201A ILE* 3.2 31.8 - - + +
249A HIS* 6.0 1.8 - - + +
262A GLY 3.7 6.5 - - - +
263A LEU* 2.7 42.1 + - + +
265A ASN* 1.3 68.0 - - - +
267A LEU* 1.3 54.1 + - - -
268A ASN 3.0 9.6 + - - -
269A TRP* 3.3 17.8 + - - +
366A VAL* 4.2 17.7 - - + -
374A PRO* 3.7 28.0 - - + -
376A GLU 3.9 19.3 - - - +
377A THR* 4.1 9.6 - - + +
378A ARG* 3.9 22.9 - - - +
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Residues in contact with LEU 267 (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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146A ASP* 5.7 0.9 - - - +
197A LYS* 2.9 40.6 + - - +
198A THR* 4.7 5.6 - - - +
201A ILE* 4.1 8.1 - - + -
249A HIS* 4.0 26.2 - - + +
250A LYS* 3.8 32.8 - - + -
253A VAL* 3.4 37.9 - - + -
254A VAL* 5.9 0.4 - - + -
263A LEU 4.2 1.8 - - - +
264A ARG* 2.9 15.7 + - + +
266A LEU* 1.3 76.0 - - - +
268A ASN* 1.3 61.3 + - - +
269A TRP 3.4 2.9 - - - -
271A HIS* 3.9 5.2 + - - -
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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