Contacts of the helix formed by residues 184 - 195 (chain D) in PDB entry 4NEF
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 184 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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20D THR* 5.2 0.4 - - - +
23D PHE* 3.4 25.4 - - + -
52D ILE* 5.2 2.0 - - - +
67D ILE 2.8 24.8 + - - -
68D ASN* 3.4 17.2 - - - +
69D PRO* 3.4 5.0 - - - +
182D SER* 2.7 26.0 + - - +
183D MET* 1.3 80.7 - - + +
185D PRO* 1.4 68.1 - - - +
186D ALA* 3.0 24.5 + - - +
187D ARG* 3.2 22.7 + - + +
188D SER 3.4 4.9 + - - -
208D PRO* 4.0 0.8 - - - +
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Residues in contact with PRO 185 (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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68D ASN* 3.4 14.6 - - - +
69D PRO* 3.8 13.7 - - + -
70D ALA* 3.8 17.3 - - + +
184D ASN* 1.4 83.3 - - - +
186D ALA* 1.3 53.0 + - - +
188D SER* 3.7 3.0 + - - -
189D LEU* 3.2 27.7 + - - +
204D PHE 3.6 18.4 - - - +
205D TRP* 3.6 44.6 - - + -
208D PRO* 4.0 10.3 - - + -
209D LEU* 4.4 11.4 - - + -
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Residues in contact with ALA 186 (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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20D THR* 4.1 8.3 - - + -
69D PRO* 3.7 19.9 - - + +
93D GLN 3.9 14.6 - - - +
94D LEU* 4.1 12.1 - - + -
97D ALA* 3.3 28.5 - - + +
184D ASN* 3.0 11.2 + - - +
185D PRO* 1.3 72.3 - - - +
187D ARG* 1.4 59.9 + - - +
188D SER 3.2 1.8 - - - -
189D LEU* 4.1 1.0 - - - +
190D ALA* 3.1 24.6 + - - +
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Residues in contact with ARG 187 (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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23D PHE* 4.1 15.3 - - + -
24D VAL* 4.0 15.0 - - + +
28D LEU* 3.5 21.7 - - + +
31D ALA* 5.4 1.2 - - - +
48D PHE* 3.7 35.9 - - + -
117D ALA* 2.8 34.1 + - - +
118D VAL 4.8 0.8 - - - -
119D ASN* 3.2 33.2 + - - +
172D HIS* 5.6 0.2 - - - -
180D GLY 4.3 8.5 + - - -
181D CYS 3.4 17.2 + - - -
182D SER* 4.0 10.8 - - - +
184D ASN* 3.2 25.6 + - + +
186D ALA* 1.4 74.1 - - - +
188D SER* 1.3 53.4 + - - +
190D ALA* 4.8 0.2 - - - -
191D PRO* 3.1 20.0 - - - +
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Residues in contact with SER 188 (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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118D VAL* 5.4 0.5 - - - +
119D ASN* 2.6 31.8 + - - +
182D SER* 2.7 22.2 + - - -
184D ASN 3.4 1.0 + - - -
185D PRO 3.8 8.7 - - - -
187D ARG* 1.3 78.2 - - - +
189D LEU* 1.4 62.4 + - - +
191D PRO* 3.4 9.2 - - - +
192D ALA* 3.3 9.7 + - - +
201D HIS* 3.2 21.8 - - - -
204D PHE* 3.2 24.1 - - - +
205D TRP* 4.9 0.2 - - - -
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Residues in contact with LEU 189 (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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94D LEU* 3.8 31.9 - - + -
98D VAL* 4.8 8.7 - - + -
185D PRO 3.2 16.1 + - - +
186D ALA* 3.5 3.8 + - - +
188D SER* 1.4 77.6 - - - +
190D ALA* 1.4 56.1 + - - +
192D ALA* 3.2 1.2 + - - +
193D VAL* 2.8 60.4 + - + +
198D PHE* 4.1 12.1 - - + -
201D HIS* 3.7 20.1 - - + +
205D TRP* 4.0 14.6 - - + +
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Residues in contact with ALA 190 (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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24D VAL* 3.8 9.0 - - + -
97D ALA* 3.3 34.1 - - + +
98D VAL* 3.7 12.6 - - - +
101D ALA* 3.7 8.5 - - + -
186D ALA 3.1 17.5 + - - +
189D LEU* 1.4 74.7 - - - +
191D PRO* 1.4 68.2 - - + +
193D VAL* 3.6 2.1 + - - +
194D VAL* 3.3 27.7 + - - +
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Residues in contact with PRO 191 (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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28D LEU* 3.8 17.0 - - + -
101D ALA* 4.1 1.0 - - + -
116D LEU* 3.2 36.6 - - + +
118D VAL* 3.6 27.1 - - + -
187D ARG* 3.1 32.5 - - - +
188D SER 3.4 9.9 - - - +
190D ALA* 1.4 84.7 - - + +
192D ALA* 1.4 55.8 + - - +
193D VAL 3.4 0.2 - - - -
194D VAL* 3.9 0.4 - - + -
195D THR* 2.8 38.6 + - - +
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Residues in contact with ALA 192 (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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118D VAL* 3.9 4.0 - - + +
188D SER 3.3 17.5 - - - +
189D LEU 3.2 4.9 + - - +
191D PRO* 1.4 77.7 - - - +
193D VAL* 1.4 61.3 + - - +
195D THR 3.0 18.5 - - - +
196D GLY* 3.4 3.6 - - - -
197D LYS 3.4 24.6 + - - +
198D PHE* 3.2 26.5 - - + -
201D HIS* 3.5 17.7 - - + -
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Residues in contact with VAL 193 (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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98D VAL* 4.2 20.9 - - + -
189D LEU* 2.8 48.2 + - + +
190D ALA 4.0 2.9 - - - +
192D ALA* 1.4 75.0 - - - +
194D VAL* 1.4 67.1 + - + +
196D GLY* 4.3 3.5 + - - -
198D PHE* 4.0 12.5 - - + -
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Residues in contact with VAL 194 (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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98D VAL* 4.0 8.1 - - + +
101D ALA* 3.8 4.3 - - + +
102D ALA* 3.8 30.1 - - + +
105D HIS* 4.1 25.6 - - + -
116D LEU* 3.9 21.8 - - + -
190D ALA 3.3 17.6 + - - +
191D PRO 4.1 2.2 - - - +
193D VAL* 1.4 83.1 - - + +
195D THR* 1.3 63.8 + - + +
196D GLY 3.8 1.4 + - - -
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Residues in contact with THR 195 (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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105D HIS* 5.6 6.1 - - + -
113D ARG* 6.1 1.8 - - + -
114D GLY 4.2 13.2 - - - +
115D ASP* 3.4 20.3 + - - -
116D LEU* 3.8 21.7 - - + +
118D VAL* 3.7 1.6 - - - +
191D PRO 2.8 29.4 + - - +
192D ALA 3.0 4.0 - - - +
194D VAL* 1.3 79.3 - - + +
196D GLY* 1.3 53.2 + - - +
197D LYS* 2.7 29.2 + - - +
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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