Contacts of the strand formed by residues 181 - 189 (chain B) in PDB entry 1QM4
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 181 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26B VAL* 3.6 7.1 - - - +
27B GLY* 2.9 32.2 + - - +
30B HIS* 4.3 0.3 - - - +
162B ASN* 2.6 28.5 + - - +
165B MET* 4.5 6.8 - - - +
179B PRO 3.5 3.9 + - - -
180B ASP* 1.3 83.8 + - - +
182B LYS* 1.3 63.3 + - - +
207B SER 3.2 13.9 - - - -
208B VAL* 3.9 16.6 - - - -
251B PHE* 4.8 3.4 - - - -
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Residues in contact with LYS 182 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135A ASP* 4.7 15.6 + - - +
24B GLU* 3.5 24.8 + - - +
25B SER 3.7 11.7 - - - +
26B VAL* 4.4 11.0 - - + -
30B HIS* 5.5 5.4 - - + +
162B ASN* 4.2 0.8 + - - +
181B SER* 1.3 75.8 - - - +
183B THR* 1.3 71.6 + - - +
184B GLN* 3.8 26.4 + - - +
205B VAL 4.0 0.3 - - - +
206B ILE* 3.5 3.5 - - - +
207B SER* 2.8 39.1 + - - +
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Residues in contact with THR 183 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B GLU* 3.0 7.3 - - - +
25B SER 3.0 29.5 + - - -
158B ALA* 3.3 32.7 + - + +
161B LEU* 3.5 28.8 - - + +
162B ASN* 3.2 31.6 + - - -
182B LYS* 1.3 75.6 + - - +
184B GLN* 1.3 68.0 + - - +
185B VAL* 4.1 1.1 - - + -
205B VAL 3.4 6.1 - - - +
206B ILE* 4.2 10.7 - - - +
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Residues in contact with GLN 184 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135A ASP* 4.4 7.2 - - - +
136A GLN* 2.9 39.7 + - + +
22B THR* 4.5 11.4 - - + +
23B SER 3.2 7.4 - - - +
24B GLU* 3.6 21.3 + - + +
182B LYS* 3.8 28.9 + - - +
183B THR* 1.3 78.2 - - - +
185B VAL* 1.3 63.6 + - - +
186B THR* 5.3 1.6 - - - -
203B THR 4.9 0.2 - - - -
204B ILE* 3.5 4.3 - - - +
205B VAL* 2.8 57.2 + - + +
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Residues in contact with VAL 185 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B THR* 4.2 0.4 - - - -
23B SER 2.9 21.2 + - - -
154B THR* 3.0 35.4 + - - +
157B LEU* 4.0 17.5 - - + -
158B ALA* 3.7 19.5 - - - +
161B LEU* 3.6 30.1 - - + -
183B THR* 4.1 0.2 - - + -
184B GLN* 1.3 76.2 - - - +
186B THR* 1.3 62.1 + - - +
187B VAL* 3.9 21.8 - - + -
201B VAL* 4.5 12.1 - - + -
203B THR 3.9 2.9 - - - -
204B ILE* 4.8 5.2 - - + -
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Residues in contact with THR 186 (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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136A GLN* 3.2 31.1 + - + +
329A LEU* 4.8 1.2 - - - +
20B MET* 4.3 16.3 - - - +
21B PHE 3.2 5.3 + - - -
22B THR* 3.1 27.7 + - + +
184B GLN 5.3 1.3 - - - -
185B VAL* 1.3 75.0 - - - +
187B VAL* 1.3 54.7 + - - +
201B VAL* 3.6 2.6 - - - -
202B HIS* 2.8 39.9 + - - +
203B THR* 2.9 35.1 + - + +
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Residues in contact with VAL 187 (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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20B MET* 3.7 2.0 - - - -
21B PHE 2.9 28.7 + - - -
153B LEU* 4.2 16.6 - - + -
154B THR* 4.4 7.9 - - - +
157B LEU* 4.7 0.2 - - + -
185B VAL* 3.9 13.0 + - + -
186B THR* 1.3 76.3 - - - +
188B GLN* 1.3 70.9 + - - +
189B TYR* 3.3 33.4 - - + +
198B PRO* 3.8 18.8 - - + -
200B ARG 3.2 11.4 - - - +
201B VAL* 3.8 26.7 - - + -
202B HIS* 4.8 0.2 - - - -
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Residues in contact with GLN 188 (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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19B PHE 3.9 4.7 - - - +
20B MET* 3.3 25.6 - - + +
187B VAL* 1.3 74.5 - - - +
189B TYR* 1.3 62.5 + - - +
199B VAL* 2.9 30.1 + - + +
200B ARG* 2.6 53.9 + - + +
202B HIS* 3.3 22.0 + - + +
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Residues in contact with TYR 189 (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 ALA* 3.2 21.9 - - - +
19B PHE* 2.9 41.3 + + + +
21B PHE* 4.1 5.2 - - + -
146B GLU* 2.6 29.5 + - - -
153B LEU* 3.5 11.3 + - - +
154B THR* 3.7 6.7 + - - -
187B VAL* 3.3 36.1 - - + -
188B GLN* 1.3 77.7 - - - +
190B VAL* 1.3 68.0 + - - +
196B VAL* 3.1 28.7 - - + -
197B ILE 3.4 7.4 - - - -
198B PRO* 3.5 23.6 - - + -
199B VAL* 4.2 2.9 - - - +
275B TRP* 3.2 28.8 - + - -
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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