Contacts of the helix formed by residues 154 - 159 (chain D) in PDB entry 6NFJ
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 SER 154 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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93D ALA* 4.2 3.2 - - - +
97D GLU* 3.7 13.7 + - - -
105D LYS* 3.3 24.4 - - - -
152D SER 4.0 1.8 + - - -
153D ILE* 1.3 75.0 - - - +
155D TRP* 1.3 58.1 + - - +
156D PRO* 3.5 4.7 - - - +
157D ARG* 2.8 33.9 + - - +
158D LEU* 3.7 2.8 + - - +
175D TYR* 2.9 20.5 + - - -
197D ASP* 3.1 28.6 + - - -
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Residues in contact with TRP 155 (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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153D ILE 3.0 7.2 + - - +
154D SER* 1.3 70.2 - - - +
156D PRO* 1.3 64.6 - - + +
157D ARG 3.1 1.4 + - - -
158D LEU* 3.4 2.4 + - - +
159D PHE* 3.0 27.0 + + - +
162D GLY* 3.3 34.1 + - - -
193D LEU 4.9 2.0 - - - +
194D TYR* 4.1 19.1 - + - -
197D ASP 3.4 15.1 + - - +
198D LEU* 4.4 15.9 - - + -
199D PRO* 3.7 20.6 - - + -
202D LEU* 4.0 10.8 - - + -
209D TRP* 4.9 2.7 - + - -
214D ILE* 4.7 4.0 - - + -
217D ILE* 4.0 10.5 - - + -
218D PHE* 3.7 40.2 - + + -
221D TYR* 3.4 61.9 - + + +
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Residues in contact with PRO 156 (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 LYS* 3.3 8.0 - - - +
106D GLY* 3.0 49.6 + - - +
107D PRO 4.1 3.6 - - - +
108D SER* 4.0 18.8 - - - -
154D SER* 3.5 14.4 - - - +
155D TRP* 1.3 92.8 - - + +
157D ARG* 1.3 58.7 + - - +
159D PHE 3.2 12.3 - - - +
160D PRO* 3.7 16.3 - - - +
197D ASP 3.5 13.9 - - - +
199D PRO* 4.1 8.9 - - + -
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Residues in contact with ARG 157 (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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93D ALA 5.1 0.4 + - - -
97D GLU* 2.5 37.4 + - - +
98D GLY 3.0 19.2 + - - -
99D SER* 2.6 34.6 + - - -
102D LYS 4.6 3.6 + - - -
103D ASP* 6.1 0.4 - - - -
105D LYS* 3.6 30.2 - - - +
131D TYR* 3.9 31.7 - - + -
154D SER* 2.8 26.9 + - - +
156D PRO* 1.3 78.4 - - - +
158D LEU* 1.3 59.9 + - - +
168D ASN* 3.3 25.8 + - - +
171D GLY* 3.9 15.3 - - - -
175D TYR* 3.7 21.4 + - + +
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Residues in contact with LEU 158 (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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153D ILE* 3.8 27.4 - - + -
154D SER 3.7 2.0 + - - +
155D TRP 3.4 3.0 + - - +
157D ARG* 1.3 78.0 - - - +
159D PHE* 1.3 72.9 + - + +
160D PRO* 3.9 0.6 - - - +
166D VAL 4.5 0.5 - - - +
167D ALA* 3.5 8.1 - - + -
168D ASN* 2.7 38.1 + - - +
171D GLY 3.8 7.6 - - - +
172D LEU* 3.7 38.6 - - + +
175D TYR* 3.9 12.1 - - + -
221D TYR* 4.2 15.3 - - + -
224D TYR* 4.6 11.7 - - + -
225D CYS* 4.4 11.4 - - - -
229D PHE* 4.4 11.4 - - + -
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Residues in contact with PHE 159 (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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155D TRP* 3.0 23.9 + - - +
156D PRO* 3.2 5.0 - - - +
158D LEU* 1.3 80.0 - - + +
160D PRO* 1.3 69.6 - - + +
161D ASP* 3.1 2.6 + - - +
162D GLY 3.8 12.6 + - - +
163D ILE 3.7 15.7 - - - +
164D VAL* 3.8 29.4 - - + -
165D THR 3.6 25.4 - - - -
166D VAL 4.5 1.8 - - - -
167D ALA* 3.6 26.0 - - + -
221D TYR* 3.6 35.4 - + - -
224D TYR* 3.4 44.4 - + + -
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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