Contacts of the helix formed by residues 165 - 174 (chain T) in PDB entry 5A0Q
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 165 (chain T).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34T ALA* 5.7 1.8 - - - -
160T SER* 3.5 21.1 - - - -
161T ILE* 3.1 21.0 + - - -
162T GLY 2.8 23.7 + - - -
163T ALA 4.2 0.9 - - - -
164T ARG* 1.3 75.8 - - - +
166T GLN* 1.3 63.6 + - - +
167T SER 3.3 0.9 - - - -
168T ALA* 3.1 6.2 + - - +
169T ARG* 2.9 50.3 + - - +
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Residues in contact with GLN 166 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30T LYS* 5.3 10.7 - - - +
164T ARG* 3.2 2.8 - - - -
165T SER* 1.3 84.7 - - - +
167T SER* 1.4 52.4 + - - +
169T ARG* 3.5 27.8 + - - +
170T THR* 2.7 32.3 + - - -
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Residues in contact with SER 167 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164T ARG* 4.0 17.7 + - - +
165T SER 3.3 0.4 - - - -
166T GLN* 1.4 74.3 - - - +
168T ALA* 1.4 61.3 + - - +
170T THR* 3.4 16.6 + - - -
171T TYR* 3.4 13.0 + - - +
197T GLU* 3.3 38.9 + - - +
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Residues in contact with ALA 168 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36T VAL* 4.8 7.9 - - + -
160T SER* 3.6 21.5 - - - +
164T ARG 4.2 3.1 + - - +
165T SER* 3.1 13.7 + - - +
167T SER* 1.4 77.7 - - - +
169T ARG* 1.3 61.8 + - - +
171T TYR* 3.5 12.5 - - - +
172T LEU* 3.4 21.8 - - - +
194T ALA* 3.9 21.1 - - + +
197T GLU* 4.0 10.2 - - + +
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Residues in contact with ARG 169 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146T GLN* 4.6 5.5 + - - +
159T MET* 4.0 21.9 - - + +
160T SER* 3.2 34.1 + - - +
161T ILE* 4.9 3.6 - - - +
165T SER* 2.9 29.5 + - - +
166T GLN* 3.7 26.6 - - - +
168T ALA* 1.3 73.8 - - - +
170T THR* 1.4 60.8 + - - +
171T TYR 3.2 0.4 - - - -
172T LEU* 3.2 20.4 + - + +
173T GLU* 2.8 28.5 - - - +
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Residues in contact with THR 170 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166T GLN 2.7 19.5 + - - -
167T SER* 3.6 12.1 - - - -
168T ALA 3.3 0.4 - - - -
169T ARG* 1.4 74.9 - - - +
171T TYR* 1.3 63.7 - - - +
173T GLU* 3.0 23.2 + - - +
174T ARG* 4.7 8.1 - - - +
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Residues in contact with TYR 171 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167T SER 3.4 9.2 + - - +
168T ALA* 3.5 10.3 - - - +
170T THR* 1.3 79.4 - - - +
172T LEU* 1.4 66.4 + - + +
173T GLU 3.6 0.7 + - - -
174T ARG* 3.4 21.2 + - - +
175T HIS* 2.8 57.7 + + - -
179T PHE* 3.8 11.1 - + - -
190T HIS* 3.0 37.0 + - - +
193T ARG* 3.6 30.6 - - + +
194T ALA* 3.5 34.8 - - + -
197T GLU* 4.6 14.4 - - + -
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Residues in contact with LEU 172 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36T VAL* 5.2 10.5 - - + -
38T LEU* 5.6 2.9 - - + -
158T ALA* 4.2 27.6 - - + -
159T MET* 4.6 16.4 - - - +
160T SER* 5.3 0.9 - - - -
168T ALA 3.4 21.1 - - - +
169T ARG* 3.2 17.1 + - + +
171T TYR* 1.4 85.4 - - + +
173T GLU* 1.3 64.5 + - - +
174T ARG 3.1 2.2 - - - -
175T HIS* 3.2 21.4 + - + +
179T PHE* 3.6 34.5 - - + -
194T ALA* 5.3 2.7 - - + -
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Residues in contact with GLU 173 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169T ARG* 2.8 22.0 - - - +
170T THR* 3.0 30.7 - - - +
171T TYR 3.6 0.6 - - - -
172T LEU* 1.3 78.1 - - - +
174T ARG* 1.3 63.0 + - + +
175T HIS 3.2 1.7 + - - -
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Residues in contact with ARG 174 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170T THR 4.7 8.1 - - - +
171T TYR* 3.4 22.4 + - - +
172T LEU 3.1 0.6 - - - -
173T GLU* 1.3 83.5 - - + +
175T HIS* 1.3 90.3 + - - +
178T GLU* 2.4 25.4 - - - +
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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