Contacts of the helix formed by residues 162 - 168 (chain B) in PDB entry 1Q6X
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 MET 162 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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20B GLU* 2.9 14.1 + - - +
146B LEU* 3.8 17.3 - - + +
147B PRO 3.4 25.1 - - - +
148B THR* 4.1 15.3 - - + +
149B ASP* 3.5 34.1 - - - +
160B LEU 3.7 9.0 - - - +
161B CYS* 1.3 72.7 - - - +
163B LYS* 1.3 66.1 + - - +
164B GLN* 3.2 2.9 - - - -
165B TYR* 3.1 47.1 + - + +
166B TYR* 3.4 27.5 - - + +
452B ARG* 3.7 6.5 - - - -
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Residues in contact with LYS 163 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18B TRP 5.2 1.7 + - - -
19B GLU* 3.6 23.8 + - - +
20B GLU* 3.5 27.0 + - + -
161B CYS* 3.2 23.8 - - - -
162B MET* 1.3 77.5 - - - +
164B GLN* 1.3 64.1 + - + +
166B TYR* 3.2 24.5 + - + +
167B ARG* 3.8 29.4 + - - +
456B GLU* 4.7 26.4 + - + -
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Residues in contact with GLN 164 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161B CYS* 5.4 4.1 + - - +
162B MET 3.1 1.9 + - - -
163B LYS* 1.3 76.8 - - + +
165B TYR* 1.3 62.6 + - + +
167B ARG* 3.2 37.7 + - - +
168B LEU* 3.6 10.7 + - - +
336B PRO 4.3 0.4 - - - -
337B PHE* 3.6 18.4 - - + +
338B ASP* 2.8 40.6 + - - +
341B VAL* 3.7 27.4 - - + +
452B ARG* 3.9 20.7 - - - +
457B GLY 3.6 14.3 + - - -
458B ARG* 3.6 22.6 - - - +
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Residues in contact with TYR 165 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137B TYR* 3.4 25.6 - - - -
141B LEU* 3.4 27.3 - - + +
146B LEU* 3.7 12.1 - - + -
149B ASP* 2.8 30.4 + - - -
162B MET* 3.1 43.0 + - + +
164B GLN* 1.3 77.1 - - + +
166B TYR* 1.3 61.0 + - + +
167B ARG 3.1 4.6 + - - -
168B LEU* 3.3 29.4 + - + +
341B VAL* 3.7 37.0 - - + +
344B GLN* 3.5 27.7 - - + +
452B ARG* 3.9 8.7 + - - -
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Residues in contact with TYR 166 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141B LEU* 3.6 47.8 - - + +
142B ASP* 5.9 0.2 - - - -
144B HIS* 3.4 38.2 - + - +
146B LEU* 5.1 9.9 + - + +
162B MET* 3.4 36.9 - - + +
163B LYS* 3.2 13.0 + - + +
165B TYR* 1.3 77.6 - - + +
167B ARG* 1.3 63.6 + - + +
168B LEU 3.5 0.2 - - - -
169B PHE 5.3 0.7 - - - -
170B SER* 2.9 15.9 + - - -
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Residues in contact with ARG 167 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163B LYS* 3.9 31.0 + - - +
164B GLN* 3.2 27.9 + - - +
165B TYR 3.1 1.0 - - - -
166B TYR* 1.3 82.3 - - + +
168B LEU* 1.3 64.9 + - - +
169B PHE 3.3 3.0 + - - -
170B SER* 3.7 5.6 - - - +
171B SER* 2.8 39.1 + - - +
182B LEU* 4.8 12.0 - - - +
336B PRO* 2.9 36.1 + - + +
337B PHE* 4.0 7.6 - - - -
458B ARG* 3.9 17.1 - - - +
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Residues in contact with LEU 168 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137B TYR* 3.9 15.9 - - + -
164B GLN 3.6 6.2 + - - +
165B TYR* 3.3 32.4 + - + +
167B ARG* 1.3 80.0 - - - +
169B PHE* 1.3 72.7 + - + +
277B ILE 4.7 0.7 - - - +
316B LYS* 5.5 0.2 + - - -
317B SER* 3.9 10.9 - - - -
318B LEU* 3.5 31.9 + - + +
337B PHE* 3.7 36.8 - - + -
341B VAL* 4.4 8.7 - - + -
342B LEU* 4.8 5.4 - - + -
345B CYS* 3.9 34.3 - - + -
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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