Contacts of the strand formed by residues 181 - 191 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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12A TYR* 3.5 25.7 + - + +
13A ALA 2.9 25.5 + - - +
179A ILE* 3.1 5.4 - - - +
180A LYS* 1.3 90.0 - - + +
182A ILE* 1.3 66.7 + - - +
183A TYR* 3.6 21.9 + - + +
205A TYR* 5.0 0.9 - - - -
208A ILE* 3.9 10.3 - - - -
225A ILE* 4.0 10.3 - - + -
226A TYR 3.2 14.4 - - - +
227A LYS* 4.2 12.3 - - + +
285B GLU* 3.2 25.8 + - - +
286B GLU* 2.9 26.0 + - - +
289B ASP* 2.6 28.2 + - - -
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Residues in contact with ILE 182 (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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13A ALA* 3.3 12.1 - - + +
15A CYS* 4.2 7.6 - - - -
174A LEU* 4.0 23.6 - - + -
179A ILE* 3.9 11.7 - - + -
181A LYS* 1.3 80.1 - - - +
183A TYR* 1.3 60.1 + - - +
184A PHE* 3.3 24.7 + - + -
197A PHE* 4.2 23.3 - - + -
200A ILE* 3.9 25.4 - - + -
205A TYR* 4.5 13.0 - - + -
225A ILE* 3.4 4.9 - - - -
226A TYR* 3.0 43.7 + - + -
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Residues in contact with TYR 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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12A TYR* 4.1 32.5 - + + -
13A ALA 2.7 17.7 + - - +
14A ILE* 3.1 21.5 - - + +
15A CYS* 2.9 28.4 + - - +
57A TYR* 3.9 21.8 - - + +
61A VAL* 4.7 4.9 - - + -
160A LYS* 5.1 2.4 + - - -
162A PHE* 4.2 18.6 - + - -
181A LYS* 3.6 23.1 + - + +
182A ILE* 1.3 69.9 - - - +
184A PHE* 1.3 59.0 + - - +
185A THR* 4.1 0.4 - - - -
224A ILE 3.7 3.1 - - - -
225A ILE* 3.6 24.2 - - + -
285B GLU 5.2 0.7 + - - -
289B ASP* 2.6 30.3 + - - -
292B TYR* 3.5 25.3 + + - -
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Residues in contact with PHE 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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15A CYS* 3.4 18.4 - - - -
17A CYS* 3.4 26.7 - - + -
34A ASN 5.1 2.5 - - - -
37A PHE* 3.1 31.2 - - + -
57A TYR* 6.1 0.4 - - - -
182A ILE* 4.2 7.6 - - + -
183A TYR* 1.3 71.7 - - - +
185A THR* 1.3 76.4 + - - +
186A ARG* 3.8 22.5 + - + -
197A PHE* 3.9 20.2 - + - -
200A ILE* 4.5 5.8 - - + -
223A PHE* 3.7 3.1 - - - +
224A ILE* 2.9 46.2 + - + +
226A TYR* 3.7 34.5 - + + -
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Residues in contact with THR 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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15A CYS 2.9 13.9 + - - -
16A ALA* 3.6 4.7 - - - -
17A CYS 2.8 28.2 + - - +
54A ASP* 2.9 29.1 + - - +
57A TYR* 4.2 2.9 - - - -
183A TYR 5.1 0.5 + - - -
184A PHE* 1.3 77.8 - - - +
186A ARG* 1.3 62.5 + - - +
187A ILE* 3.8 24.7 - - + -
221A LEU* 4.2 6.3 - - + -
222A ASP 3.6 6.1 - - - +
223A PHE* 3.3 28.5 - - + -
609A CP6 3.2 9.0 + - - -
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Residues in contact with ARG 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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17A CYS 3.8 3.6 - - - -
34A ASN* 4.5 10.9 + - - +
37A PHE* 3.9 32.1 - - + -
184A PHE* 3.8 24.0 - - + +
185A THR* 1.3 72.7 - - - +
187A ILE* 1.3 59.8 + - - +
188A ASN 3.3 2.3 + - - -
207A ILE* 5.2 0.6 - - - +
210A VAL* 4.1 6.3 - - - +
221A LEU* 3.0 28.5 - - - +
222A ASP* 2.8 50.5 + - - +
224A ILE* 3.6 36.8 - - + +
226A TYR* 5.8 0.2 - - - -
567A ILE* 4.9 6.3 + - - +
568A PRO 2.9 27.9 + - - -
569A TYR* 3.8 14.8 - - - +
570A PRO* 3.4 16.4 - - + +
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Residues in contact with ILE 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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16A ALA* 4.5 0.9 - - + -
17A CYS 2.9 20.4 + - - +
18A CYS* 3.4 20.0 - - + -
19A LYS 3.9 0.3 + - - -
37A PHE* 3.8 6.2 - - - -
48A TRP* 4.1 37.9 - - + -
51A ASN* 4.5 12.3 - - - +
54A ASP* 4.7 4.0 - - + -
185A THR* 3.8 23.3 - - + -
186A ARG* 1.3 69.1 - - - +
188A ASN* 1.3 59.6 + - - +
189A SER* 2.8 28.0 + - - +
191A TYR* 4.2 12.8 - - + +
219A THR* 4.2 13.2 - - + +
220A THR 4.2 2.5 - - - -
221A LEU* 4.1 16.4 - - + -
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Residues in contact with ASN 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 LYS* 3.0 24.1 + - - +
37A PHE* 3.9 5.5 - - - -
186A ARG 3.3 2.2 + - - -
187A ILE* 1.3 69.1 - - - +
189A SER* 1.3 59.3 + - - +
219A THR* 3.4 5.3 + - - -
220A THR* 2.9 29.9 + - - +
570A PRO* 3.1 30.2 + - + -
571A PHE 2.9 25.7 + - - -
595A ASN* 3.0 38.8 + - - +
597A VAL* 3.3 12.3 - - - +
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Residues in contact with SER 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 CYS* 3.5 9.2 - - - +
19A LYS* 3.0 29.7 + - - +
187A ILE* 2.8 8.0 + - - +
188A ASN* 1.3 75.0 - - - +
190A THR* 1.3 61.2 + - - +
191A TYR* 2.7 36.6 + - - -
218A ASN 5.6 0.9 - - - -
219A THR* 2.8 18.6 + - - -
595A ASN* 3.3 18.6 - - - -
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Residues in contact with THR 190 (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 LYS* 3.3 28.4 + - - +
20A VAL 3.7 3.3 + - - +
21A GLU* 3.3 43.5 - - + +
22A SER 4.8 0.9 - - - +
189A SER* 1.3 73.5 - - - +
191A TYR* 1.3 77.9 + - - +
595A ASN* 4.1 3.2 + - - -
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Residues in contact with TYR 191 (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 CYS* 3.8 12.3 - - + -
19A LYS 3.5 3.7 + - - +
21A GLU* 3.5 23.4 + - - -
47A PRO* 3.4 36.1 - - + +
48A TRP* 3.5 28.6 - - + +
187A ILE* 4.2 7.5 - - + +
189A SER* 2.7 47.8 + - - -
190A THR* 1.3 79.9 - - - +
192A GLU* 1.3 65.0 + - - +
193A CYS* 3.4 12.1 + - - -
217A ASN 5.2 2.8 + - - -
218A ASN 5.2 1.2 + - - -
219A THR* 4.1 13.0 - - - +
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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