Contacts of the helix formed by residues 229 - 244 (chain D) in PDB entry 2NMP
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 CYS 229 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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204D ASP* 5.3 7.3 + - + +
227D VAL* 3.8 2.9 - - - +
228D ASN* 1.3 77.2 - - + +
230D GLU* 1.3 69.0 + - - +
231D SER* 4.0 9.4 - - - -
232D LEU* 3.2 34.1 + - + +
233D HIS* 2.9 25.2 + - - +
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Residues in contact with GLU 230 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82D LYS* 3.8 19.7 + - - +
83D TYR* 2.6 39.4 + - - -
228D ASN 3.4 3.5 + - - +
229D CYS* 1.3 75.4 - - - +
231D SER* 1.3 64.6 + - - +
233D HIS* 3.1 16.8 + - - +
234D ASN* 3.2 27.0 + - - +
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Residues in contact with SER 231 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229D CYS* 3.5 9.2 - - - -
230D GLU* 1.3 79.0 - - - +
232D LEU* 1.3 63.2 + - - +
234D ASN* 3.8 12.5 + - - +
235D ARG* 3.2 33.1 + - - +
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Residues in contact with LEU 232 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100D LEU* 3.6 33.0 - - + -
183D ILE* 4.1 19.1 - - + -
204D ASP* 3.9 25.8 - - + +
205D ILE* 3.9 11.2 - - + -
227D VAL* 3.8 22.9 - - + -
229D CYS* 3.2 25.0 + - + +
231D SER* 1.3 80.7 + - - +
233D HIS* 1.3 58.2 + - - +
235D ARG* 3.4 10.8 + - + +
236D LEU* 3.0 32.6 + - + +
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Residues in contact with HIS 233 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83D TYR* 3.4 57.4 - + + +
85D LEU* 4.2 9.6 - - + +
227D VAL* 4.2 10.4 - - + +
229D CYS 2.9 12.1 + - - +
230D GLU* 3.3 10.8 - - - +
232D LEU* 1.3 72.9 - - - +
234D ASN* 1.3 71.1 + - - +
236D LEU* 3.1 7.7 + - - +
237D ARG* 2.6 82.4 + - + +
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Residues in contact with ASN 234 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230D GLU* 3.2 25.5 + - - +
231D SER* 4.1 12.2 - - - +
232D LEU 3.5 0.2 - - - -
233D HIS* 1.3 89.0 - - - +
235D ARG* 1.3 57.3 + - + +
237D ARG* 3.4 7.2 + - - +
238D PHE* 3.1 30.3 + - - +
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Residues in contact with ARG 235 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100D LEU* 2.7 54.8 + - + +
101D LEU* 4.7 4.2 - - - +
181D ASP* 4.8 11.9 + - - -
183D ILE* 4.5 17.3 - - - +
231D SER* 3.2 29.3 + - - +
232D LEU* 3.5 11.2 - - - +
233D HIS 3.1 0.4 - - - -
234D ASN* 1.3 77.6 - - + +
236D LEU* 1.3 62.6 + - - +
238D PHE* 3.8 6.0 + - - +
239D LEU* 3.3 28.6 + - - +
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Residues in contact with LEU 236 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85D LEU* 3.7 18.2 - - + +
87D PHE* 5.1 4.0 - - + -
96D THR* 4.7 6.5 - - + +
97D ILE* 4.5 16.6 - - + -
100D LEU* 3.4 36.6 - - + -
205D ILE* 3.9 15.0 - - + -
225D VAL* 4.1 18.4 - - + -
227D VAL* 4.4 13.5 - - + -
232D LEU* 3.0 32.1 + - + +
233D HIS 3.1 7.2 + - - +
235D ARG* 1.3 75.2 - - - +
237D ARG* 1.3 65.6 + - - +
239D LEU* 3.0 8.3 + - + +
240D GLN* 2.9 22.3 + - - +
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Residues in contact with ARG 237 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63D SER 5.2 7.7 + - - +
68D ARG* 5.1 1.2 - - - +
69D ASN* 6.4 0.2 - - - -
72D GLU* 2.8 34.2 + - - -
83D TYR* 5.1 1.4 - - - +
84D CYS 3.4 12.3 + - - -
85D LEU* 3.4 24.6 - - - +
233D HIS* 2.6 52.2 + - + +
234D ASN* 3.7 9.4 - - - +
236D LEU* 1.3 71.8 - - - +
238D PHE* 1.3 64.0 + - - +
240D GLN* 2.8 32.9 + - - +
241D ASN* 3.2 21.7 + - - +
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Residues in contact with PHE 238 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119C ARG* 4.0 19.7 - - + -
123C GLN* 3.5 32.1 - - + -
124C VAL* 4.1 20.0 - - + -
234D ASN 3.1 17.4 + - - +
235D ARG* 3.9 7.0 - - - +
236D LEU 3.2 0.2 - - - -
237D ARG* 1.3 77.2 - - - +
239D LEU* 1.3 67.6 + - + +
241D ASN* 3.4 7.9 + - + +
242D SER* 2.9 51.2 + - - -
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Residues in contact with LEU 239 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124C VAL* 4.3 19.3 - - + -
96D THR* 3.6 33.3 - - + +
99D HIS* 3.8 29.6 - - + +
100D LEU* 3.6 22.7 - - + -
235D ARG 3.3 16.8 + - - +
236D LEU* 3.0 8.3 + - + +
238D PHE* 1.3 89.5 - - + +
240D GLN* 1.3 64.0 + - - +
241D ASN 3.1 0.2 - - - -
242D SER* 4.3 1.3 - - - +
243D LEU* 2.9 39.9 + - + +
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Residues in contact with GLN 240 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62D ARG 5.2 0.4 - - - -
63D SER 4.6 2.8 - - - +
68D ARG* 3.6 28.0 + - - +
72D GLU* 3.1 20.6 + - - -
85D LEU* 4.1 6.2 - - + +
86D ALA 3.0 27.0 + - - +
87D PHE* 3.8 27.8 - - + -
96D THR* 4.1 1.2 - - - +
236D LEU 2.9 11.2 + - - +
237D ARG* 2.8 38.3 + - - +
239D LEU* 1.3 78.2 - - - +
241D ASN* 1.3 57.4 + - - +
244D GLY* 3.5 17.0 + - - -
245D ALA 4.3 2.2 + - - +
246D VAL* 3.8 15.6 - - + +
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Residues in contact with ASN 241 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91C LEU* 3.5 0.3 - - - +
119C ARG* 3.4 33.9 - - - +
62D ARG* 3.2 39.3 + - - +
63D SER* 2.5 43.1 + - - +
237D ARG 3.2 8.9 + - - +
238D PHE* 3.8 9.2 - - - +
239D LEU 3.1 0.4 - - - -
240D GLN* 1.3 80.5 + - - +
242D SER* 1.3 63.1 + - - +
243D LEU 3.5 0.4 + - - -
244D GLY 3.8 1.4 + - - -
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Residues in contact with SER 242 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91C LEU* 3.2 18.6 - - - +
95C VAL* 4.4 1.2 - - - +
116C GLY 4.7 0.3 - - - +
119C ARG* 3.3 30.8 + - - +
120C TYR* 4.2 17.8 - - - +
124C VAL* 4.6 13.5 - - - -
238D PHE* 2.9 43.3 + - - -
239D LEU* 4.3 3.4 - - - -
241D ASN* 1.3 77.2 + - - +
243D LEU* 1.3 62.1 + - - +
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Residues in contact with LEU 243 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91C LEU* 3.5 4.6 - - - +
92C ALA* 3.3 23.2 + - - +
95C VAL* 3.7 17.2 - - + +
120C TYR* 3.8 29.8 - - + -
124C VAL* 3.8 16.8 - - + -
95D VAL* 4.8 3.1 - - + -
96D THR* 3.9 32.3 - - + +
99D HIS* 3.8 32.3 - - + +
239D LEU* 2.9 24.6 + - + +
242D SER* 1.3 78.2 - - - +
244D GLY* 1.3 62.8 + - - +
245D ALA* 3.3 8.6 + - + +
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Residues in contact with GLY 244 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88C ALA* 3.8 4.2 - - - +
89C SER* 2.6 32.8 + - - -
91C LEU* 4.3 1.8 - - - -
92C ALA* 3.8 1.9 - - - +
62D ARG* 4.0 18.6 - - - -
240D GLN 3.5 16.1 + - - -
241D ASN 3.8 1.1 + - - -
242D SER 3.4 2.2 - - - -
243D LEU* 1.3 78.2 - - - +
245D ALA* 1.3 54.8 + - - +
246D VAL* 2.8 15.3 + - - +
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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