Contacts of the strand formed by residues 181 - 191 (chain B) in PDB entry 3QGT
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 LYS 181 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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285A GLU* 3.9 14.7 + - - +
286A GLU* 4.0 11.3 - - - +
289A ASP* 2.7 27.9 + - - -
12B TYR* 3.4 27.6 - - + +
13B ALA 2.8 26.6 + - - +
179B ILE* 3.3 3.5 - - - +
180B LYS* 1.3 88.3 - - + +
182B ILE* 1.3 65.7 + - - +
183B TYR* 3.7 24.1 + - + +
205B TYR* 5.5 0.2 - - - -
208B ILE* 3.9 13.6 - - - +
225B ILE* 4.0 10.8 - - + -
226B TYR 3.2 12.6 - - - +
227B LYS* 3.4 30.0 - - + +
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Residues in contact with ILE 182 (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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13B ALA* 2.9 14.6 - - + +
15B CYS* 4.3 7.0 - - - -
174B LEU* 3.9 25.1 - - + -
179B ILE* 3.5 15.5 - - + -
181B LYS* 1.3 76.1 - - - +
183B TYR* 1.3 54.7 + - - +
184B PHE* 2.7 33.6 + - + +
197B PHE* 4.1 22.4 - - + -
200B ILE* 3.8 22.7 - - + -
205B TYR* 4.4 15.3 - - + -
224B ILE 3.6 0.3 - - - +
226B TYR* 2.9 43.3 + - + +
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Residues in contact with TYR 183 (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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285A GLU 5.1 0.2 + - - -
289A ASP* 2.4 32.4 + - - -
292A TYR* 3.5 30.0 + + - -
12B TYR* 4.3 20.2 - + + -
13B ALA 2.7 13.8 + - - +
14B ILE* 3.3 22.3 - - + +
15B CYS 3.1 27.2 + - - +
57B TYR* 3.6 25.1 - - + +
61B VAL* 4.3 13.5 - - + -
160B LYS* 4.9 5.9 + - - -
162B PHE* 4.7 9.0 - + - -
181B LYS* 3.7 33.5 + - + +
182B ILE* 1.3 68.1 - - - +
184B PHE* 1.3 59.5 + - - +
185B THR* 4.6 1.4 + - - -
224B ILE 3.8 6.3 - - - -
225B ILE* 4.0 16.8 - - + +
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Residues in contact with PHE 184 (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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15B CYS* 3.4 20.6 - - - -
17B CYS* 3.3 25.8 - - + -
34B ASN 5.1 3.4 - - - -
37B PHE* 2.9 33.4 - - + -
57B TYR* 6.0 0.2 - - - -
182B ILE* 2.7 11.4 + - + +
183B TYR* 1.3 70.5 - - - +
185B THR* 1.3 78.1 + - - +
186B ARG* 3.7 20.3 + - + -
197B PHE* 4.4 15.3 - + - -
200B ILE* 4.4 5.4 - - + -
223B PHE* 3.8 1.2 - - - -
224B ILE* 2.9 44.1 + - + +
226B TYR* 3.6 39.3 - + + -
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Residues in contact with THR 185 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B CYS 3.0 14.9 + - - -
16B ALA* 3.4 3.3 - - + -
17B CYS 2.8 30.1 + - - +
54B ASP* 3.0 26.8 + - - +
57B TYR* 3.9 5.0 - - - -
183B TYR 4.6 0.3 + - - -
184B PHE* 1.3 76.6 - - - +
186B ARG* 1.3 63.2 + - - +
187B ILE* 3.7 23.8 - - + -
221B LEU* 4.3 4.5 - - + -
222B ASP 3.7 6.1 - - - +
223B PHE* 3.0 32.6 - - + -
609B CP6 3.4 8.0 + - - -
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Residues in contact with ARG 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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17B CYS 3.7 3.4 - - - -
34B ASN* 4.8 6.8 + - - -
37B PHE* 3.8 31.4 - - + -
184B PHE* 3.7 23.8 - - + -
185B THR* 1.3 70.2 - - - +
187B ILE* 1.3 62.0 + - - +
188B ASN 3.4 1.4 + - - -
207B ILE* 5.2 0.4 - - - +
210B VAL* 4.6 3.8 - - - +
221B LEU* 3.1 26.6 - - - +
222B ASP* 2.7 53.4 + - - +
224B ILE* 3.4 39.6 - - + +
323B HIS* 4.7 2.0 - - - -
567B ILE* 4.9 5.9 - - - +
568B PRO 3.0 28.1 + - - -
569B TYR* 3.8 19.6 - - - -
570B PRO* 3.6 13.0 - - + +
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Residues in contact with ILE 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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16B ALA* 4.6 0.9 - - + -
17B CYS 2.8 25.1 + - - +
18B CYS* 3.4 21.6 - - + -
19B LYS 4.0 0.3 + - - -
37B PHE* 3.7 6.9 - - - -
48B TRP* 4.2 30.7 - - + -
51B ASN* 4.2 18.6 - - - +
54B ASP* 4.6 7.6 - - + -
185B THR* 3.7 24.9 - - + -
186B ARG* 1.3 69.2 - - - +
188B ASN* 1.3 58.6 + - - +
189B SER* 2.9 27.3 + - - +
191B TYR* 4.3 11.0 - - + +
219B THR* 4.0 15.9 - - + -
220B THR 4.2 2.0 - - - -
221B LEU* 4.2 8.3 - - + -
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Residues in contact with ASN 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 LYS* 2.9 25.3 + - - +
37B PHE* 3.8 6.1 - - - -
186B ARG 3.4 2.0 + - - -
187B ILE* 1.3 66.7 - - - +
189B SER* 1.3 61.1 + - - +
219B THR* 3.2 7.4 + - - -
220B THR* 3.1 28.6 + - - +
570B PRO* 3.5 27.0 + - + -
571B PHE 3.1 22.8 + - - -
572B PRO* 4.1 0.2 - - - +
595B ASN* 2.7 44.2 + - - +
597B VAL* 3.2 11.6 - - - +
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Residues in contact with SER 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 CYS* 3.5 1.7 - - - +
19B LYS* 3.1 25.4 + - - +
187B ILE* 2.9 8.8 + - - +
188B ASN* 1.3 74.7 - - - +
190B THR* 1.3 61.5 + - - +
191B TYR* 2.9 44.6 + - - -
218B ASN 5.6 0.4 - - - -
219B THR* 2.8 21.6 + - - -
595B ASN* 3.5 16.8 - - - +
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Residues in contact with THR 190 (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 LYS* 3.4 21.0 + - - +
20B VAL 3.5 8.7 + - - +
21B GLU* 3.5 42.3 - - + +
26B GLY 4.6 11.9 + - - +
27B LYS* 5.4 4.7 - - - +
189B SER* 1.3 71.9 - - - +
191B TYR* 1.3 75.7 + - - +
595B ASN* 4.1 5.2 + - - +
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Residues in contact with TYR 191 (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 CYS* 3.7 17.7 - - + -
19B LYS 3.1 9.8 + - - +
21B GLU* 3.8 18.3 + - - -
47B PRO* 3.4 39.0 - - + +
48B TRP* 3.5 29.5 - - + +
187B ILE* 4.3 2.6 - - + +
189B SER* 2.9 47.5 + - - -
190B THR* 1.3 79.0 - - - +
192B GLU* 1.3 64.3 + - - +
193B CYS* 3.3 12.5 + - - -
217B ASN 5.2 2.8 + - - -
218B ASN 5.4 0.3 + - - -
219B THR* 4.2 11.8 - - - +
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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