Contacts of the helix formed by residues 156 - 170 (chain B) in PDB entry 6CQE
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 PHE 156 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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174A GLY* 6.1 6.3 - - - -
135B HIS* 3.7 19.2 + - + +
136B ARG* 3.6 37.0 - - + -
137B ASP* 3.2 43.3 - - + -
142B ASN* 4.7 4.3 - - - +
154B ALA 3.7 1.8 + - - -
155B ASP* 1.3 74.4 + - - +
157B GLY* 1.3 62.1 + - - +
158B ILE 3.3 2.4 + - - -
159B SER* 3.4 7.5 + - - -
160B ALA* 2.9 54.9 + - + +
192B TYR* 4.1 18.4 - + - -
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Residues in contact with GLY 157 (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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62B GLU* 3.6 14.9 - - - +
136B ARG* 3.6 30.0 - - - +
155B ASP* 3.1 8.0 + - - -
156B PHE* 1.3 78.9 - - - +
158B ILE* 1.3 61.6 + - - +
160B ALA* 3.5 6.3 + - - +
161B GLN* 3.3 27.5 + - - +
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Residues in contact with ILE 158 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46B LYS* 5.0 8.1 - - - +
59B LEU* 4.3 15.7 - - + +
62B GLU* 3.9 22.4 - - + +
63B ILE* 3.7 32.8 - - + -
66B LEU* 4.4 18.8 - - + -
77B TYR* 5.5 0.7 - - + -
89B ILE* 4.7 28.7 - - + -
91B MET* 6.1 0.7 - - - -
155B ASP* 2.8 22.5 + - + +
157B GLY* 1.3 69.2 - - - -
159B SER* 1.3 67.8 + - - +
161B GLN* 3.1 14.8 + - - +
162B ILE* 3.1 31.1 + - + +
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Residues in contact with SER 159 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28B TYR* 3.2 36.3 + - - -
46B LYS* 4.6 17.9 + - - +
155B ASP* 4.1 7.7 + - - -
156B PHE* 3.4 13.4 + - - -
158B ILE* 1.3 80.5 - - - +
160B ALA* 1.3 56.5 + - - +
162B ILE* 3.3 8.1 + - - -
163B GLY 2.9 25.3 + - - -
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Residues in contact with ALA 160 (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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172A PHE 4.5 3.4 - - - +
28B TYR* 5.2 1.8 - - - -
156B PHE* 2.9 49.5 + - + +
157B GLY* 3.7 6.7 - - - +
158B ILE 3.2 0.2 - - - -
159B SER* 1.3 77.8 - - - +
161B GLN* 1.3 62.1 + - + +
163B GLY* 3.3 2.6 + - - -
164B ALA* 2.9 28.8 + - - +
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Residues in contact with GLN 161 (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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221A LEU* 3.7 39.2 - - + +
225A PHE* 5.2 0.6 - - - -
59B LEU* 3.6 22.2 - - + -
62B GLU* 3.4 32.5 + - + -
136B ARG* 6.0 0.2 - - - +
157B GLY 3.3 13.6 + - - +
158B ILE 3.1 4.0 + - - +
160B ALA* 1.3 76.5 - - - +
162B ILE* 1.3 65.6 + - - +
164B ALA* 3.4 11.5 + - - +
165B THR* 3.1 27.4 + - - -
168B ARG* 5.0 4.5 + - - -
188B LEU* 4.9 8.9 - - - +
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Residues in contact with ILE 162 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28B TYR* 4.0 22.4 - - + -
46B LYS* 5.8 4.9 - - + -
48B VAL* 4.1 35.0 - - + -
50B MET* 6.4 1.8 - - + -
59B LEU* 4.4 19.1 - - + -
87B LEU* 4.7 1.8 - - + -
89B ILE* 6.0 1.1 - - + -
158B ILE* 3.1 32.5 + - + +
159B SER* 3.6 9.4 - - - +
161B GLN* 1.3 77.4 - - - +
163B GLY* 1.3 61.7 + - - +
165B THR* 3.2 8.4 + - - -
166B LEU* 3.0 34.3 + - + +
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Residues in contact with GLY 163 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172A PHE* 3.2 33.4 - - - +
28B TYR* 3.3 21.7 + - - -
159B SER 2.9 10.9 + - - -
160B ALA 3.6 2.7 - - - -
162B ILE* 1.3 76.2 - - - +
164B ALA* 1.3 61.7 + - - +
166B LEU* 3.3 4.0 + - - +
167B ALA* 3.0 18.0 + - - +
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Residues in contact with ALA 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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172A PHE 3.7 2.6 + - - -
173A ILE* 5.3 4.0 - - + -
160B ALA 2.9 16.5 + - - +
161B GLN* 3.8 11.7 - - - +
162B ILE 3.3 0.2 - - - -
163B GLY* 1.3 75.0 - - - +
165B THR* 1.3 58.1 + - - +
167B ALA* 3.1 4.6 + - - +
168B ARG* 2.8 58.2 + - - +
173B ILE* 3.8 12.5 - - + +
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Residues in contact with THR 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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219A HIS* 4.0 22.5 - - + +
221A LEU* 5.5 2.4 - - - +
54B ASP* 3.6 14.1 - - - +
161B GLN 3.1 14.6 + - - -
162B ILE* 3.5 10.1 - - - -
164B ALA* 1.3 74.2 - - - +
166B LEU* 1.3 59.0 + - + +
168B ARG* 3.3 20.6 + - - +
169B ARG* 2.9 54.8 + - - +
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Residues in contact with LEU 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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172A PHE* 3.8 30.7 - - + -
28B TYR* 3.7 35.4 - - + -
162B ILE* 3.0 28.4 + - + +
163B GLY 3.5 5.4 - - - +
165B THR* 1.3 76.8 - - + +
167B ALA* 1.3 62.3 + - - +
169B ARG* 3.1 30.3 + - - +
170B LEU* 3.0 28.0 + - + +
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Residues in contact with ALA 167 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167A ALA* 4.3 8.1 - - + -
172A PHE* 3.7 23.6 - - + -
173A ILE* 4.7 2.5 - - + -
163B GLY 3.0 13.4 + - - +
164B ALA* 3.5 7.9 - - - +
166B LEU* 1.3 75.7 - - - +
168B ARG* 1.3 61.2 + - - +
170B LEU 3.4 1.0 + - - -
171B ALA 3.0 3.5 + - - -
172B PHE* 2.9 31.6 + - + -
173B ILE* 3.5 29.5 + - + -
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Residues in contact with ARG 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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219A HIS* 5.3 0.2 - - - -
220A PRO* 3.7 33.6 - - + +
221A LEU* 4.6 12.5 - - - +
224A LEU* 3.7 27.0 - - - +
161B GLN* 5.0 7.1 + - - -
164B ALA* 2.8 48.0 + - - +
165B THR* 3.6 22.6 + - - +
167B ALA* 1.3 69.8 - - - +
169B ARG* 1.3 66.3 + - - +
171B ALA* 3.0 13.5 + - - +
173B ILE* 3.8 19.2 - - + +
174B GLY 3.7 23.4 + - - +
175B THR* 4.5 9.6 - - - +
176B PRO* 4.5 2.2 - - - +
187B ALA* 5.5 6.1 + - - +
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Residues in contact with ARG 169 (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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51B GLU* 3.3 29.1 - - - +
53B ASP* 2.8 39.0 + - - +
54B ASP* 3.2 29.1 + - - -
165B THR* 2.9 28.2 + - - +
166B LEU* 3.1 35.6 + - - +
168B ARG* 1.3 77.8 - - - +
170B LEU* 1.3 69.3 + - + +
171B ALA* 3.2 2.0 + - - +
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Residues in contact with LEU 170 (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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170A LEU* 5.1 2.7 - - + -
172A PHE* 3.7 31.0 - - + -
166B LEU* 3.0 15.7 + - + +
167B ALA 4.2 1.1 - - - +
168B ARG 3.2 0.2 - - - -
169B ARG* 1.3 85.7 - - + +
171B ALA* 1.3 69.4 + - - +
172B PHE* 3.2 36.1 + - + -
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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