Contacts of the strand formed by residues 243 - 248 (chain A) in PDB entry 1NSX
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 ASP 243 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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71A ARG* 4.8 1.6 - - - -
198A LEU* 3.3 22.5 - - - +
203A GLU* 2.7 18.4 - - - +
239A VAL* 4.0 19.3 - - + +
242A ILE* 1.3 72.8 - - - +
244A HIS* 1.3 69.4 + - - +
245A PRO* 4.5 0.3 - - - +
277A VAL* 4.6 3.3 - - - +
278A ILE 3.2 4.7 - - - -
279A PHE* 3.3 27.6 - - + +
282A ASN* 4.1 2.0 - - - +
1400A GAL 2.5 45.3 + - - -
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Residues in contact with HIS 244 (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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195A PHE* 3.4 27.1 - + + -
196A VAL 3.4 20.6 - - - -
198A LEU* 3.8 13.6 - - + +
217A LEU* 5.6 2.8 - - + +
235A GLN* 2.8 50.3 + - + -
236A VAL* 5.4 0.7 - - + -
239A VAL* 3.9 10.3 - - + +
241A GLY 4.8 0.7 - - - -
242A ILE* 3.9 9.2 - - + +
243A ASP* 1.3 101.6 + - - +
245A PRO* 1.3 66.6 - - + +
246A PHE* 3.2 25.0 - - + -
277A VAL* 4.1 4.8 - - - +
278A ILE 2.9 32.2 + - - -
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Residues in contact with PRO 245 (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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195A PHE* 3.4 5.4 - - - +
196A VAL* 3.1 51.4 + - + +
198A LEU* 4.7 7.4 - - + -
205A VAL* 5.4 2.2 - - + -
243A ASP 4.5 1.3 - - - +
244A HIS* 1.3 87.9 - - + +
246A PHE* 1.3 61.8 + - - +
247A LEU* 5.1 0.2 - - + -
275A SER* 4.3 2.9 - - - +
276A ILE 3.6 6.3 - - - +
277A VAL* 4.0 14.4 - - + -
308A SER* 3.2 31.9 - - - +
309A PRO* 3.8 19.3 - - + +
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Residues in contact with PHE 246 (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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190A LEU* 3.6 27.4 - - + -
192A ALA* 3.8 16.2 - - + -
194A ARG 3.6 5.6 - - - -
195A PHE* 4.0 25.8 - + + -
212A ILE* 4.6 7.0 - - + -
217A LEU* 4.0 35.4 - - + -
219A PHE* 5.3 3.8 - + - -
242A ILE* 3.7 29.4 - - + -
244A HIS* 3.2 24.5 - - + -
245A PRO* 1.3 73.9 - - - +
247A LEU* 1.3 62.7 + - - +
248A LEU* 3.6 1.8 + - + +
275A SER* 3.2 7.1 - - - -
276A ILE* 2.9 36.3 + - + +
278A ILE* 4.0 17.5 - - + -
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Residues in contact with LEU 247 (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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192A ALA* 3.0 18.7 - - - +
193A SER 4.0 1.0 + - - -
194A ARG* 2.8 52.0 + - + +
196A VAL* 4.2 14.6 - - + -
209A ILE* 3.7 30.7 - - + -
245A PRO 5.0 0.4 - - - +
246A PHE* 1.3 74.0 - - - +
248A LEU* 1.3 64.6 + - - +
249A ASP* 3.5 4.3 + - - +
274A PRO* 4.0 4.0 - - + +
275A SER* 4.1 15.9 - - - -
308A SER* 4.1 8.5 - - - +
317A LEU* 4.0 30.3 - - + -
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Residues in contact with LEU 248 (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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190A LEU* 4.3 14.1 - - + -
191A ALA 3.6 9.0 - - - +
192A ALA* 4.5 2.2 - - + -
194A ARG* 5.1 4.9 + - - -
246A PHE 4.7 2.7 - - - +
247A LEU* 1.3 75.7 - - - +
249A ASP* 1.3 64.3 + - - +
250A GLN 4.4 0.7 - - - +
251A LEU* 3.8 19.1 - - + +
257A GLN* 3.8 39.0 - - + +
271A THR* 4.1 7.6 - - + -
273A GLN 3.5 24.0 - - - +
274A PRO 3.1 19.4 + - - +
275A SER* 4.2 3.8 - - - -
276A ILE* 4.0 32.5 - - + -
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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