Contacts of the helix formed by residues 252 - 256 (chain S) in PDB entry 6NZO
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 252 (chain S).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106S PHE* 3.7 11.1 - - - -
108S VAL* 3.5 22.4 - - - +
109S ILE 3.0 25.3 + - - +
110S SER* 5.6 1.1 + - - -
177S LYS* 4.5 10.2 + - - -
207S TYR* 2.6 31.6 + - + -
208S GLU 4.8 1.9 - - - +
209S TYR* 6.1 1.0 - - - -
210S VAL* 3.8 23.2 + - + +
247S ALA* 4.8 0.4 - - - +
251S GLY* 1.3 74.8 - - - +
253S LEU* 1.3 72.7 + - - +
254S GLY 3.1 10.5 + - - +
255S ARG* 3.4 24.7 - - - +
256S PHE* 4.5 0.3 - - - -
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Residues in contact with LEU 253 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91S LEU 5.8 0.4 - - - -
92S PHE* 4.3 15.3 - - + -
108S VAL* 5.1 9.2 - - + -
182S VAL* 5.1 10.5 - - + +
183S SER* 6.0 1.8 - - - -
184S VAL* 4.1 13.9 - - + -
194S LEU* 3.3 17.7 - - + +
207S TYR* 3.4 29.4 - - + +
252S ASN* 1.3 92.0 + - - +
254S GLY* 1.3 56.5 + - - +
255S ARG 3.2 2.9 + - - -
256S PHE* 3.2 41.5 - - + -
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Residues in contact with GLY 254 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194S LEU* 4.3 11.0 - - - -
207S TYR* 3.8 15.8 - - - -
208S GLU 4.8 2.4 + - - -
209S TYR* 3.8 27.6 - - - -
235S TYR* 5.6 0.5 - - - -
252S ASN* 3.1 4.0 + - - +
253S LEU* 1.3 75.2 - - - +
255S ARG* 1.3 62.9 + - - +
256S PHE 3.4 0.7 - - - -
257S CYS* 4.4 11.3 - - - +
280S ILE* 5.1 7.9 - - - +
294S PHE* 5.8 1.9 - - - -
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Residues in contact with ARG 255 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103S CYS* 3.2 36.7 - - - +
104S ARG* 3.5 21.2 + - - +
106S PHE* 3.4 35.4 - - - -
209S TYR* 4.5 2.9 - - + -
235S TYR* 2.6 51.6 + - + +
247S ALA* 3.4 41.6 + - + -
248S THR* 3.9 12.5 + - - +
252S ASN 3.4 20.0 - - - +
253S LEU 3.2 1.8 - - - -
254S GLY* 1.3 79.2 - - - +
256S PHE* 1.3 67.9 + - + +
257S CYS* 2.8 17.5 + - - +
296S TYR* 4.7 0.2 + - - -
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Residues in contact with PHE 256 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91S LEU 4.3 3.1 - - - -
92S PHE* 3.7 26.9 - - + -
103S CYS* 3.6 20.0 - - + -
106S PHE* 4.4 1.1 - + - -
184S VAL* 3.6 30.5 - - + -
192S TYR* 2.9 48.0 - + + +
193S GLY* 3.6 1.7 - - - -
194S LEU* 3.2 39.4 + - + +
235S TYR* 4.6 1.8 - - - -
252S ASN 4.5 2.2 - - - -
253S LEU* 3.2 38.8 + - + -
254S GLY 3.4 1.6 - - - -
255S ARG* 1.3 95.4 - - - +
257S CYS* 1.3 58.8 + - - +
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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