Contacts of the helix formed by residues 252 - 259 (chain A) in PDB entry 3NX4
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 VAL 252 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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251A THR* 1.3 71.9 - - - +
253A MSE 1.3 62.9 + - - +
254A PRO* 3.4 1.1 - - - -
255A PHE* 3.0 15.2 + - + +
256A ILE* 2.9 54.5 + - + +
220B GLY* 4.0 15.9 - - - -
221B ASP 4.5 0.2 - - - +
224B LEU* 3.8 28.5 - - + -
239B ALA* 5.8 1.3 - - + -
241B GLY 4.0 9.2 - - - +
242B LEU* 4.2 2.7 - - + -
246B PHE* 2.9 34.5 + - + +
247B ALA 4.1 7.2 - - - +
248B LEU* 4.2 5.2 - - + -
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Residues in contact with MSE 253 (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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206A PRO* 3.9 14.1 - - + -
207A LEU* 3.9 20.8 - - + +
251A THR* 3.1 19.3 - - - +
252A VAL* 1.3 78.1 - - - +
254A PRO* 1.3 66.8 - - + +
256A ILE* 4.2 9.0 - - - -
257A LEU* 2.9 57.8 + - + +
242B LEU* 4.1 26.2 - - + -
246B PHE* 4.2 17.3 - - + -
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Residues in contact with PRO 254 (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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206A PRO 3.7 16.2 - - - +
207A LEU* 3.8 12.5 - - + -
228A LEU* 3.4 40.6 - - + +
229A ALA* 4.2 0.7 - - + -
250A THR* 4.8 3.1 - - - +
251A THR* 3.3 20.9 - - - +
252A VAL 3.6 0.4 - - - -
253A MSE 1.3 95.8 - - + +
255A PHE* 1.3 61.6 + - + +
258A ARG* 3.1 30.3 + - + +
260A VAL* 3.3 22.1 + - + +
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Residues in contact with PHE 255 (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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228A LEU* 3.9 31.4 - - + -
250A THR* 4.5 2.5 - - + -
251A THR 3.6 25.4 - - - -
252A VAL* 3.0 11.6 + - - +
254A PRO* 1.3 82.9 - - + +
256A ILE* 1.3 63.7 + - + +
259A ASN* 3.0 19.4 + - - -
260A VAL* 3.4 29.2 - - + +
262A LEU* 3.8 24.9 - - + -
239B ALA* 4.8 6.3 - - + +
248B LEU* 4.2 8.7 - - + -
262B LEU* 3.6 37.9 - - + -
264B GLY* 3.1 30.2 - - - -
265B VAL 3.3 0.5 + - - -
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Residues in contact with ILE 256 (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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252A VAL* 2.9 37.2 + - + +
253A MSE 4.2 5.2 - - - +
255A PHE* 1.3 78.7 - - + +
257A LEU* 1.3 76.8 + - + +
239B ALA* 3.7 9.9 - - + +
240B CYS* 3.4 42.2 - - - +
241B GLY* 3.7 4.7 - - - +
242B LEU* 3.8 34.3 - - + -
265B VAL 3.6 6.7 - - - -
266B ASP* 3.4 16.0 - - - +
330B NAP 3.3 18.9 + - + +
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Residues in contact with LEU 257 (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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207A LEU* 3.7 27.4 - - + -
233A TYR* 3.6 14.4 - - - -
253A MSE 2.9 44.8 + - + +
256A ILE* 1.3 96.4 - - + +
258A ARG* 1.3 64.0 + - + +
259A ASN 3.7 1.1 - - - -
42B LYS* 6.1 2.0 - - - +
266B ASP* 3.7 13.7 - - - +
268B VAL* 5.5 7.2 - - + -
269B MSE 4.1 8.8 - - - +
330B NAP 6.1 1.3 - - - +
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Residues in contact with ARG 258 (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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207A LEU* 3.9 39.0 - - + +
208A GLU 2.9 30.1 + - - -
209A LYS* 4.8 0.8 - - - +
210A GLN* 3.4 38.4 - - - +
228A LEU 6.0 0.4 - - - -
229A ALA 3.0 18.8 + - - -
231A MSE 3.6 18.0 + - - -
233A TYR* 3.4 20.1 - - + +
234A GLY 2.8 31.4 + - - -
253A MSE 3.7 0.2 + - - -
254A PRO* 3.1 16.1 + - - +
257A LEU* 1.3 86.3 - - + +
259A ASN* 1.3 60.4 + - - +
260A VAL* 3.1 9.3 + - + +
269B MSE 5.8 1.6 - - + -
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Residues in contact with ASN 259 (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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233A TYR* 4.0 23.4 + - + +
234A GLY* 3.6 15.9 - - - +
255A PHE 3.0 16.2 + - - -
257A LEU 3.7 1.2 - - - -
258A ARG* 1.3 79.7 - - - +
260A VAL* 1.3 64.2 + - - +
261A ARG 3.7 0.7 + - - -
133B LEU* 5.8 0.3 - - - +
263B GLN* 3.4 12.2 + - - +
264B GLY 3.4 15.2 + - - +
265B VAL* 3.4 4.2 - - - +
266B ASP* 2.8 32.7 + - - +
270B THR* 6.1 0.2 - - - +
271B PRO* 6.6 0.2 - - - -
274B ARG* 6.1 2.2 - - - +
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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