Contacts of the helix formed by residues 157 - 171 (chain B) in PDB entry 1YQZ
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 GLY 157 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155B GLY 3.8 1.4 - - - -
156B ALA* 1.3 80.7 - - - +
158B TYR* 1.3 67.3 + - - -
159B VAL* 3.2 7.5 + - - -
160B SER* 3.2 5.7 + - - -
161B LEU* 3.0 21.7 + - - +
184B ASN* 4.6 8.1 - - - -
185B LYS* 5.5 4.3 - - - -
236B GLY 5.2 2.4 + - - -
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Residues in contact with TYR 158 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131B ARG* 5.6 2.3 + - - -
157B GLY* 1.3 71.5 - - - -
159B VAL* 1.3 96.9 + - + +
161B LEU* 3.3 6.3 + - - +
162B GLU* 2.9 37.6 + - - +
184B ASN* 4.4 8.3 + - - +
186B LEU* 4.7 20.0 - - + -
293B PRO 4.1 4.7 + - - -
294B LEU* 3.7 25.7 - - + +
325B ILE 5.6 3.4 - - - -
326B VAL* 3.7 32.3 - - + -
440B FAD 3.6 48.8 + + - -
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Residues in contact with VAL 159 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46B PRO* 4.9 1.0 - - - +
130B LEU* 5.7 4.7 - - + +
131B ARG* 4.9 8.5 - - - +
157B GLY* 4.6 6.3 - - - +
158B TYR* 1.3 105.2 - - + +
160B SER* 1.3 81.3 + - - +
162B GLU* 3.2 5.5 + - - +
163B VAL* 2.9 30.5 + - + +
236B GLY* 4.7 14.6 - - - +
238B GLY 6.3 0.4 - - - +
440B FAD 4.0 29.6 - - + -
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Residues in contact with SER 160 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153B VAL* 3.7 14.4 - - - +
154B VAL 3.1 21.7 + - - -
155B GLY 3.0 29.2 + - - -
156B ALA* 4.1 0.7 - - - -
157B GLY 3.2 7.0 + - - -
159B VAL* 1.3 82.3 - - - +
161B LEU* 1.3 59.5 + - - +
163B VAL* 3.3 6.4 + - - +
164B LEU* 2.9 30.2 + - - +
176B LEU* 5.4 0.4 - - - -
234B ILE* 6.1 1.2 - - - +
236B GLY* 3.4 17.7 + - - -
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Residues in contact with LEU 161 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156B ALA* 3.6 26.2 - - + +
157B GLY 3.0 20.3 + - - +
158B TYR* 3.8 5.6 - - - +
160B SER* 1.3 77.1 - - - +
162B GLU* 1.3 63.0 + - + +
164B LEU* 3.3 3.6 + - + +
165B GLU* 3.0 18.9 + - - +
176B LEU* 4.3 21.1 - - + -
183B ILE* 5.9 0.4 - - + -
184B ASN* 4.1 11.0 - - + +
195B ILE* 4.0 40.4 - - + -
326B VAL* 5.3 8.3 - - + -
328B PHE* 3.4 40.5 - - + -
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Residues in contact with GLU 162 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
420A ALA* 4.6 8.1 - - - +
421A PRO* 4.8 0.5 - - - +
43B CYS 4.5 3.3 - - - +
46B PRO* 3.5 27.1 - - + +
47B TYR* 3.6 28.4 + - - +
158B TYR* 2.9 28.4 + - - +
159B VAL* 3.8 3.7 - - - +
161B LEU* 1.3 75.7 - - - +
163B VAL* 1.3 62.5 + - - +
165B GLU* 3.4 5.5 + - - +
166B ASN* 2.8 34.5 + - - +
325B ILE 5.4 0.2 - - - +
326B VAL* 3.7 25.7 - - + +
327B LYS 4.4 8.5 + - - +
440B FAD 4.1 21.7 + - - +
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Residues in contact with VAL 163 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46B PRO* 4.3 12.6 - - + -
49B ILE* 4.8 7.4 - - + +
130B LEU* 3.6 32.3 - - + -
153B VAL* 4.9 3.8 - - + -
159B VAL* 2.9 23.5 + - + +
160B SER* 3.6 7.2 - - - +
162B GLU* 1.3 78.3 - - - +
164B LEU* 1.3 56.6 + - - +
166B ASN* 3.2 4.6 + - - +
167B LEU* 2.9 37.9 + - + +
234B ILE* 3.6 42.6 - - + -
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Residues in contact with LEU 164 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153B VAL* 4.3 16.1 - - + +
160B SER 2.9 16.5 + - - +
161B LEU* 3.6 7.6 - - + +
162B GLU 3.3 0.2 - - - -
163B VAL* 1.3 77.5 - - - +
165B GLU* 1.3 68.8 + - - +
167B LEU* 3.3 5.2 + - - +
168B TYR* 3.0 19.6 + - - +
174B PRO* 3.9 17.0 - - + +
176B LEU* 3.5 42.4 - - + +
199B LEU* 4.0 26.0 - - + -
204B ILE* 4.2 17.9 - - + -
328B PHE* 4.0 11.4 - - + -
329B PHE* 4.1 6.7 - - + -
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Residues in contact with GLU 165 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47B TYR* 6.2 2.2 - - - -
161B LEU 3.0 16.2 + - - +
162B GLU* 3.8 6.5 - - - +
163B VAL 3.3 0.2 - - - -
164B LEU* 1.3 77.6 - - - +
166B ASN* 1.3 62.5 + - - +
168B TYR* 3.3 3.8 + - - +
169B GLU* 2.9 37.5 + - + +
327B LYS* 2.7 38.1 + - - +
328B PHE* 3.5 9.3 - - + -
329B PHE* 2.7 63.3 + - + -
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Residues in contact with ASN 166 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46B PRO* 3.0 34.9 + - - +
47B TYR* 3.4 41.3 - - - -
49B ILE* 4.7 1.8 - - + -
50B GLY* 3.3 25.2 - - - +
52B VAL* 3.7 10.9 - - - +
162B GLU* 2.8 28.1 + - - +
163B VAL* 3.7 4.7 - - - +
165B GLU* 1.3 80.3 - - - +
167B LEU* 1.3 64.5 + - - +
169B GLU* 3.3 5.4 + - - +
170B ARG* 3.0 19.1 + - - +
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Residues in contact with LEU 167 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49B ILE* 3.9 22.9 - - + -
143B ILE* 4.4 2.5 - - + -
151B VAL* 3.8 19.3 - - + -
153B VAL* 3.8 22.9 - - + -
163B VAL* 2.9 38.2 + - + +
164B LEU* 3.3 4.7 + - - +
166B ASN* 1.3 75.7 - - - +
168B TYR* 1.3 60.4 + - - +
170B ARG* 3.3 11.1 + - - +
171B GLY 3.3 0.2 + - - -
172B LEU* 3.0 56.5 + - + +
174B PRO* 4.5 7.4 - - + -
232B MET* 4.3 8.3 - - + -
234B ILE* 3.8 9.4 - - + -
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Residues in contact with TYR 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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164B LEU 3.0 13.1 + - - +
165B GLU 3.4 7.2 - - - +
167B LEU* 1.3 77.1 - - - +
169B GLU* 1.3 84.1 + - - +
171B GLY* 2.9 20.4 + - - -
172B LEU 3.8 14.3 + - - +
173B HIS* 6.0 4.5 - + - -
174B PRO* 4.2 11.7 - - + +
202B ARG* 3.8 32.0 + - + +
204B ILE* 3.5 30.5 - - + -
329B PHE* 3.6 19.7 - + + -
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Residues in contact with GLU 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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50B GLY 4.6 6.9 - - - +
52B VAL* 5.2 10.8 - - + -
165B GLU* 2.9 32.2 + - + +
166B ASN* 3.3 7.8 + - - +
168B TYR* 1.3 98.4 - - - +
170B ARG* 1.3 60.3 + - - +
171B GLY* 3.0 1.8 + - - -
202B ARG* 5.4 0.3 + - - -
329B PHE* 3.5 15.1 - - - -
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Residues in contact with ARG 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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48B VAL 4.7 1.0 + - - -
49B ILE* 2.9 30.7 + - - +
50B GLY* 4.0 11.8 + - - +
51B GLU* 3.4 39.7 + - - +
140B ASP* 2.9 33.9 + - - +
143B ILE* 3.6 42.8 - - - +
144B LYS* 4.1 11.1 - - - +
166B ASN 3.0 16.6 + - - +
167B LEU* 3.5 8.3 - - - +
168B TYR 3.2 0.4 - - - -
169B GLU* 1.3 76.0 - - - +
171B GLY* 1.3 57.8 + - - +
172B LEU* 3.8 21.5 - - + +
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Residues in contact with GLY 171 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149B ASP* 4.8 1.9 - - - +
168B TYR 2.9 11.7 + - - -
169B GLU 3.0 2.5 - - - -
170B ARG* 1.3 80.1 - - - +
172B LEU* 1.3 69.1 + - - +
173B HIS* 4.2 13.1 + - - -
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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