Contacts of the helix formed by residues 144 - 150 (chain X) in PDB entry 3N5N
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 THR 144 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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111X ARG* 3.3 50.9 - - + +
114X TYR* 3.6 16.2 + - - -
142X TRP 3.2 0.6 - - - -
143X PRO* 1.3 83.2 - - + +
145X LEU* 1.3 65.5 + - - +
146X GLN* 3.6 16.8 + - - +
147X ASP* 2.6 35.8 + - - +
148X LEU 3.1 17.7 + - - -
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Residues in contact with LEU 145 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110X ASP* 4.5 9.6 - - + +
111X ARG* 6.1 0.4 - - - +
114X TYR* 3.4 41.1 - - + +
117X TRP* 4.0 23.6 - - + -
144X THR* 1.3 72.7 - - - +
146X GLN* 1.3 67.6 + - - +
148X LEU* 3.2 1.4 + - - -
149X ALA* 2.8 31.9 + - - +
176X ALA* 3.8 17.1 - - + +
179X VAL* 3.5 26.9 - - + -
180X VAL* 4.4 7.2 - - + -
185X GLY 3.6 15.9 - - - +
187X MET* 3.8 17.9 - - + -
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Residues in contact with GLN 146 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144X THR* 3.7 18.3 - - - +
145X LEU* 1.3 82.2 + - - +
147X ASP* 1.3 63.2 + - - +
149X ALA* 3.0 18.4 + - - +
150X SER* 3.2 15.1 + - - -
180X VAL* 4.2 16.9 - - + +
185X GLY* 4.0 29.9 + - - -
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Residues in contact with ASP 147 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141X LYS 4.6 1.3 - - - +
142X TRP* 3.4 32.5 - - + -
143X PRO* 3.4 18.6 - - - +
144X THR* 2.6 34.4 + - - +
146X GLN* 1.3 78.7 - - - +
148X LEU* 1.3 63.7 + - - +
150X SER* 3.3 13.4 + - - -
151X ALA 3.6 5.2 + - - -
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Residues in contact with LEU 148 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114X TYR* 3.6 25.4 - - + +
138X TRP* 3.6 35.4 - - + -
142X TRP* 3.9 22.8 - - + +
144X THR 3.1 7.9 + - - +
145X LEU 3.8 5.6 - - - +
147X ASP* 1.3 76.1 - - - +
149X ALA* 1.3 65.2 + - - +
151X ALA* 3.1 10.8 + - + -
156X VAL* 4.2 8.3 - - + -
172X LEU* 3.9 11.2 - - + +
173X GLN* 3.2 48.9 + - + +
176X ALA* 3.8 13.7 - - + -
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Residues in contact with ALA 149 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145X LEU 2.8 17.4 + - - +
146X GLN* 3.0 11.0 + - - +
148X LEU* 1.3 74.8 - - - +
150X SER* 1.3 58.4 + - - +
151X ALA 3.7 3.6 + - - +
173X GLN* 4.5 4.6 + - - +
176X ALA* 4.1 1.0 - - - +
177X ARG* 3.9 37.9 - - + +
180X VAL* 3.6 27.1 - - + -
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Residues in contact with SER 150 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146X GLN 3.2 12.8 + - - -
147X ASP* 3.3 7.7 + - - -
148X LEU 3.1 0.8 - - - -
149X ALA* 1.3 76.5 - - - +
151X ALA* 1.3 63.5 + - - +
152X SER 3.9 0.3 + - - -
155X GLU* 4.9 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