Contacts of the strand formed by residues 181 - 189 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26A VAL* 3.6 6.6 - - - +
27A GLY* 3.0 31.6 + - - +
30A HIS* 4.3 0.3 - - - +
162A ASN* 2.6 29.7 + - - +
165A MET* 4.5 6.8 - - - +
179A PRO 3.6 3.6 + - - -
180A ASP* 1.3 84.0 + - - +
182A LYS* 1.3 63.5 + - - +
207A SER 3.2 14.1 - - - -
208A VAL* 3.9 16.6 - - - -
251A PHE* 4.8 2.0 - - - -
401A AMB 4.6 1.7 - - - +
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Residues in contact with LYS 182 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A GLU* 3.4 24.7 - - - +
25A SER 3.7 11.2 - - - +
26A VAL* 4.4 11.9 - - + +
30A HIS* 5.8 1.8 - - + +
162A ASN* 4.3 0.8 + - - +
181A SER* 1.3 74.6 - - - +
183A THR* 1.3 72.1 + - - +
184A GLN* 3.9 16.2 - - - +
205A VAL 4.0 0.6 - - - +
206A ILE* 3.5 2.6 - - - +
207A SER* 2.9 34.0 + - - +
251A PHE* 5.6 0.2 - - - -
401A AMB 4.0 26.2 + - - +
402A SO4 3.0 41.2 + - - +
135B ASP* 4.9 6.1 + - - +
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Residues in contact with THR 183 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24A GLU* 3.1 9.4 - - - +
25A SER 3.0 27.8 + - - -
158A ALA* 3.3 33.7 - - + +
161A LEU* 3.5 28.9 - - + +
162A ASN* 3.3 30.8 + - - -
182A LYS* 1.3 74.8 + - - +
184A GLN* 1.3 66.4 + - - +
185A VAL* 4.1 2.2 - - + -
205A VAL 3.4 6.5 - - - +
206A ILE* 4.1 11.4 - - - +
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Residues in contact with GLN 184 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22A THR* 4.1 16.5 - - + +
23A SER 3.2 7.2 - - - +
24A GLU* 3.7 18.2 - - + +
182A LYS* 3.9 21.8 - - + +
183A THR* 1.3 79.5 - - - +
185A VAL* 1.3 65.8 + - - +
186A THR* 4.3 1.8 - - + -
203A THR 4.9 0.2 - - - -
204A ILE* 3.5 4.7 - - - +
205A VAL* 2.9 46.3 + - + +
402A SO4 3.1 29.6 + - - +
135B ASP* 4.5 1.0 - - - +
136B GLN* 3.1 35.3 + - + +
137B GLY* 4.7 1.4 - - - -
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Residues in contact with VAL 185 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22A THR* 4.3 0.2 - - - -
23A SER* 2.9 20.4 + - - -
154A THR* 3.0 34.0 + - - +
157A LEU* 4.0 17.7 - - + -
158A ALA* 3.7 19.7 - - - +
161A LEU* 3.6 28.5 - - + -
184A GLN* 1.3 79.4 - - - +
186A THR* 1.3 62.2 + - - +
187A VAL* 4.0 21.5 - - + -
201A VAL* 4.5 11.7 - - + -
203A THR 3.9 3.1 - - - -
204A ILE* 4.7 6.1 - - + +
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Residues in contact with THR 186 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20A MET* 4.2 17.0 - - - +
21A PHE 3.2 5.3 + - - -
22A THR* 2.9 31.3 + - + +
184A GLN 5.3 1.6 - - - +
185A VAL* 1.3 73.7 - - - +
187A VAL* 1.3 55.3 + - - +
201A VAL* 3.6 2.1 - - - -
202A HIS* 2.8 39.6 + - - +
203A THR* 2.9 39.8 + - + +
205A VAL* 6.0 0.2 - - + -
136B GLN* 3.6 25.8 - - + +
329B LEU* 5.1 1.2 - - - +
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Residues in contact with VAL 187 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20A MET* 3.6 1.7 - - - -
21A PHE 2.9 32.5 + - - -
153A LEU* 4.3 16.8 - - + -
154A THR* 4.4 8.1 - - - +
185A VAL* 4.0 13.9 + - + -
186A THR* 1.3 76.5 - - - +
188A GLN* 1.3 69.2 + - - +
189A TYR* 3.4 33.9 - - + +
198A PRO* 3.8 17.9 - - + -
200A ARG 3.3 11.9 - - - +
201A VAL* 3.8 26.7 - - + -
202A HIS* 4.7 0.7 - - - -
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Residues in contact with GLN 188 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19A PHE 3.9 4.9 - - - +
20A MET* 3.3 24.7 - - + +
187A VAL* 1.3 74.7 - - - +
189A TYR* 1.3 61.9 + - - +
199A VAL* 2.9 29.8 + - + +
200A ARG* 2.6 55.0 + - + +
202A HIS* 3.3 22.8 + - + +
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Residues in contact with TYR 189 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18A ALA* 3.2 22.2 - - - +
19A PHE* 2.8 43.8 + + + +
21A PHE* 4.1 5.8 - - + -
146A GLU* 2.6 30.4 + - - -
153A LEU* 3.5 13.3 + - - +
154A THR* 3.7 4.5 + - - -
187A VAL* 3.4 34.8 - - + -
188A GLN* 1.3 76.3 - - - +
190A VAL* 1.3 67.6 + - - +
196A VAL* 3.2 27.8 - - + -
197A ILE 3.5 6.1 - - - -
198A PRO* 3.5 24.5 - - + -
199A VAL* 4.3 2.5 - - - +
275A TRP* 3.2 29.2 - + - -
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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