Contacts of the helix formed by residues 157 - 169 (chain B) in PDB entry 1QQW
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 ASP 157 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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155B ILE* 3.8 3.5 - - - +
156B ARG* 1.3 81.6 - - + +
158B PRO* 1.3 75.7 - - - +
159B ILE* 3.3 18.8 + - - +
160B LEU* 2.9 36.9 + - + +
349B LYS* 4.0 13.6 - - - +
350B MET* 3.2 6.3 - - - +
434B THR* 4.2 7.9 + - - +
39C LEU 3.5 2.0 - - - +
40C ASN* 3.2 19.6 - - - +
41C VAL* 3.2 30.4 + - - +
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Residues in contact with PRO 158 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157B ASP* 1.3 89.8 - - - +
159B ILE* 1.3 57.8 + - - +
160B LEU 2.9 6.0 + - - -
161B PHE* 3.0 14.3 + - + +
162B PRO* 3.2 12.0 - - - +
349B LYS* 3.1 37.5 - - + +
350B MET* 3.1 17.9 - - - -
353B GLY* 4.2 7.4 - - - -
600B HEM 3.7 21.5 - - + -
41C VAL* 4.6 7.9 - - + -
50C LEU* 5.8 0.4 - - + -
57C PHE* 3.8 22.9 - - + -
61C MET* 3.9 4.7 - - + +
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Residues in contact with ILE 159 (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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157B ASP* 3.0 17.3 + - - +
158B PRO* 1.3 78.3 - - - +
160B LEU* 1.3 62.8 + - + +
162B PRO* 4.1 2.2 - - - +
431B ARG* 5.1 0.7 - - - +
38C LYS* 3.1 46.8 + - + +
39C LEU* 3.3 35.4 - - - +
40C ASN 3.5 9.2 - - - +
41C VAL* 4.6 7.2 - - + +
54C ASP* 4.9 1.6 - - - +
56C VAL* 4.6 6.7 - - + -
57C PHE* 3.6 48.1 - - + +
60C GLU* 3.2 17.8 - - - +
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Residues in contact with LEU 160 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
405A TYR 4.0 18.6 - - - +
155B ILE* 3.9 23.3 - - + -
156B ARG 5.4 0.4 - - - +
157B ASP* 2.9 36.7 + - + +
159B ILE* 1.3 84.7 - - + +
161B PHE* 1.3 56.1 + - - +
162B PRO 3.4 1.1 - - - -
163B SER* 3.0 8.7 + - - -
164B PHE* 2.7 32.6 + - - +
185B PHE* 4.0 12.6 - - + -
189B ARG* 3.5 43.7 - - - +
191B GLU* 4.5 0.9 - - - +
38C LYS* 4.6 4.3 - - - +
39C LEU* 4.1 20.9 - - + +
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Residues in contact with PHE 161 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74B VAL* 4.4 8.3 - - + -
75B HIS* 6.2 0.7 - + - -
116B VAL* 6.3 0.2 - - + -
153B PHE* 4.2 23.8 - + - -
155B ILE* 3.4 15.9 - - + +
158B PRO 3.0 10.8 + - - +
160B LEU* 1.3 76.7 - - - +
162B PRO* 1.3 73.9 - - + +
163B SER 2.9 0.9 + - - -
164B PHE* 3.0 3.0 + + - -
165B ILE* 2.9 57.6 + - + +
600B HEM 3.4 75.8 - + + -
64C PHE* 3.6 26.9 - + - -
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Residues in contact with PRO 162 (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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158B PRO 3.2 13.9 - - - +
159B ILE 4.1 4.7 - - - +
160B LEU 3.6 3.4 - - - -
161B PHE* 1.3 93.3 - - + +
163B SER* 1.3 55.2 + - - +
165B ILE* 3.9 2.3 - - - +
166B HIS* 3.1 39.5 + - + -
60C GLU* 3.9 34.5 - - + +
61C MET* 3.9 24.5 - - + -
64C PHE* 4.0 30.0 - - + -
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Residues in contact with SER 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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386A TYR* 4.8 4.7 - - - +
403A ASN 4.4 1.4 + - - -
404A TYR* 3.7 10.3 - - - +
405A TYR* 3.3 35.9 + - - +
160B LEU 3.0 9.5 + - - -
162B PRO* 1.3 75.1 - - - +
164B PHE* 1.3 66.9 + - - +
166B HIS* 2.9 10.4 + - - +
167B SER* 2.9 23.8 + - - -
185B PHE* 4.5 2.5 - - - -
38C LYS* 3.1 24.8 + - - -
60C GLU* 4.5 3.5 + - - -
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Residues in contact with PHE 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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116B VAL* 5.9 2.9 - - + -
153B PHE* 4.0 18.8 - + - -
154B PHE* 3.3 42.6 - + + -
155B ILE* 4.3 7.6 - - + -
160B LEU 2.7 18.1 + - - +
161B PHE* 3.6 8.5 - + - +
163B SER* 1.3 71.8 - - - +
165B ILE* 1.3 85.4 + - + +
167B SER* 2.4 26.7 + - - -
168B GLN* 3.2 31.2 + - + +
185B PHE* 3.5 37.3 - + + -
186B TRP* 3.4 24.7 - - - -
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Residues in contact with ILE 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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73B VAL* 4.8 0.7 - - + +
74B VAL* 3.6 28.3 - - + -
116B VAL* 4.3 14.1 - - + -
117B ALA* 6.2 0.9 - - + -
153B PHE* 5.5 0.7 - - + -
161B PHE* 2.9 52.4 + - + +
162B PRO 3.9 3.8 - - - +
164B PHE* 1.3 96.8 - - + +
166B HIS* 1.3 68.9 + - + +
168B GLN* 3.0 17.0 + - + +
169B LYS* 3.1 30.7 + - + +
64C PHE* 4.2 14.6 - - + -
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Residues in contact with HIS 166 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386A TYR 3.1 23.7 + - - -
387A GLN* 4.9 0.7 - - - -
388A ARG* 4.5 11.3 - - + +
403A ASN* 2.6 50.8 + - + +
162B PRO* 3.1 29.3 + - + -
163B SER* 2.9 9.5 + - - +
165B ILE* 1.3 76.8 - - + +
167B SER* 1.3 65.4 + - - +
169B LYS* 3.0 22.6 + - + +
170B ARG 4.5 1.6 - - - +
181B MET* 3.6 11.2 - - - +
64C PHE* 4.3 6.6 - + + -
67C GLU* 3.0 39.6 + - - -
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Residues in contact with SER 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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404A TYR* 4.5 7.8 - - - +
163B SER 2.9 11.2 + - - -
164B PHE* 2.4 27.7 + - - -
166B HIS* 1.3 78.1 - - - +
168B GLN* 1.3 67.7 + - - +
169B LYS 3.5 3.8 + - - +
178B ASP 4.7 0.5 + - - +
181B MET* 3.4 44.9 - - - +
182B VAL* 3.6 20.0 + - - +
185B PHE* 4.2 17.2 - - - +
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Residues in contact with GLN 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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116B VAL* 6.3 1.6 - - + -
117B ALA* 4.0 24.5 - - + +
128B ASP* 4.7 10.6 - - - +
154B PHE* 6.0 0.4 - - - -
164B PHE* 3.4 35.8 - - + +
165B ILE* 3.0 14.4 + - + +
167B SER* 1.3 83.1 + - - +
169B LYS* 1.3 67.3 + - - +
177B LYS* 4.2 11.4 + - - +
182B VAL* 3.7 28.3 + - - +
186B TRP* 3.4 36.9 - - - -
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Residues in contact with LYS 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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71B GLU* 6.1 1.3 - - - -
73B VAL 3.1 26.9 + - - -
74B VAL* 3.8 10.1 - - - +
76B ALA* 6.4 0.2 - - - +
116B VAL 3.6 8.1 + - - -
117B ALA* 3.4 41.2 + - + +
118B GLY 5.3 0.6 + - - -
119B GLU* 4.3 14.4 - - - +
165B ILE* 3.3 21.4 - - + +
166B HIS* 3.0 15.2 + - + +
167B SER 3.8 6.4 - - - +
168B GLN* 1.3 83.6 - - - +
170B ARG* 1.3 71.4 + - + +
177B LYS* 4.1 17.9 - - - +
178B ASP 4.4 3.3 + - - -
181B MET* 5.2 1.2 - - - +
182B VAL* 5.6 0.5 - - - +
68C ARG* 3.7 18.4 - - - +
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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