Contacts of the helix formed by residues 200 - 205 (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 LEU 200 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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107D PRO* 2.8 44.7 + - + +
108D SER 4.0 6.7 - - - +
109D ILE* 4.4 14.1 - - + +
112D HIS* 4.0 46.4 - - + +
198D LEU 3.4 2.3 + - - -
199D PRO* 1.3 72.9 - - - +
201D ALA* 1.3 58.6 + - - +
203D GLN* 2.9 23.9 + - + +
204D GLU* 3.1 37.7 + - + +
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Residues in contact with ALA 201 (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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107D PRO 4.8 0.2 + - - -
160D PRO 4.8 2.2 + - - +
161D ASP* 3.5 30.1 - - + +
199D PRO* 3.3 1.4 - - - +
200D LEU* 1.3 78.7 - - - +
202D LEU* 1.3 59.7 + - - +
204D GLU* 4.0 11.4 - - - +
205D LYS* 3.2 35.2 + - + +
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Residues in contact with LEU 202 (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* 4.0 13.7 - - + -
161D ASP* 3.6 23.1 - - + +
162D GLY* 3.6 22.7 - - - -
163D ILE* 4.7 2.0 - - + +
198D LEU* 4.4 7.0 - - + -
199D PRO* 3.4 18.9 + - + +
200D LEU 3.2 0.8 - - - -
201D ALA* 1.3 79.7 - - - +
203D GLN* 1.3 57.9 + - - +
205D LYS 4.3 1.1 - - - -
206D TYR* 3.5 37.8 + - + +
207D GLY 3.2 8.9 + - - -
208D GLY* 3.0 18.5 + - - +
214D ILE* 4.2 15.8 - - + +
217D ILE* 3.8 25.6 - - + -
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Residues in contact with GLN 203 (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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109D ILE* 3.8 31.1 - - + +
198D LEU* 4.0 3.5 - - - +
199D PRO 3.7 1.2 + - - +
200D LEU* 2.9 17.2 + - + +
202D LEU* 1.3 77.5 - - - +
204D GLU* 1.3 64.3 - - + +
205D LYS 3.4 0.8 - - - -
207D GLY* 3.3 24.7 + - - -
208D GLY* 3.4 22.8 - - - +
209D TRP* 6.0 0.2 - - - -
210D LYS* 4.9 3.4 - - - +
250D TYR* 3.2 26.3 + - - -
257D PRO* 3.4 25.8 - - + +
259D GLU* 4.6 6.1 + - - -
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Residues in contact with GLU 204 (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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112D HIS* 5.6 4.7 + - - -
200D LEU* 3.1 39.8 + - + +
201D ALA* 3.7 10.2 + - - +
203D GLN* 1.3 77.5 - - + +
205D LYS* 1.3 66.1 + - + +
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Residues in contact with LYS 205 (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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201D ALA* 3.2 22.2 + - + +
204D GLU* 1.3 81.6 - - + +
206D TYR* 1.3 84.7 + - + +
207D GLY 3.6 0.2 - - - -
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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