Contacts of the strand formed by residues 16 - 21 (chain M) in PDB entry 3HOU
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 GLU 16 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14M VAL* 3.4 7.2 - - - +
15M LYS* 1.3 84.0 - - - +
17M VAL* 1.3 65.0 - - - +
18M GLN 4.1 0.7 - - - -
1418M LEU* 3.8 20.0 - - + +
1419M ASP 3.1 12.1 - - - +
1420M ASP* 5.4 1.9 - - - +
1421M CYS* 4.0 0.4 - - - -
1215N ARG 4.0 0.2 - - - +
1217N TYR* 3.1 30.1 + - + +
1219N ASP 3.3 3.8 - - - +
1220N ARG* 3.4 29.8 + - + +
1221N SER* 2.8 27.0 + - - -
1222N ARG* 3.3 16.1 + - - +
13P ARG* 2.6 33.3 + - - -
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Residues in contact with VAL 17 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14M VAL* 3.9 10.3 - - + -
16M GLU* 1.3 79.3 - - - +
18M GLN* 1.3 59.0 + - - +
19M PHE* 3.6 33.3 + - + -
1397M LEU* 3.9 18.6 - - + -
1417M GLU 3.8 0.3 - - - +
1418M LEU* 3.5 6.9 - - - -
1419M ASP* 2.9 36.6 + - + +
1421M CYS* 3.5 21.8 - - - -
1430M LEU* 4.6 2.9 - - + -
1204N PHE* 5.3 2.0 - - + -
1214N PRO* 4.4 7.0 - - + -
1215N ARG 3.2 13.0 - - - +
1216N LEU* 4.2 15.0 - - + -
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Residues in contact with GLN 18 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16M GLU 4.1 1.4 - - - -
17M VAL* 1.3 69.6 - - - +
19M PHE* 1.3 84.2 + - - +
228M PHE* 3.3 39.7 - - + -
1416M ALA 4.1 7.2 + - - +
1417M GLU 3.9 3.6 + - - +
1418M LEU* 3.8 34.3 - - + +
1213N THR 3.2 3.5 - - - +
1214N PRO 4.8 0.2 - - - -
1215N ARG* 2.9 52.1 + - + +
1217N TYR* 3.9 18.8 - - + -
12P ARG* 4.9 4.4 - - - +
13P ARG* 4.3 8.5 - - - +
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Residues in contact with PHE 19 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17M VAL* 3.6 28.0 + - + -
18M GLN* 1.3 84.7 - - - +
20M GLY* 1.3 58.9 + - - +
228M PHE* 4.1 1.5 - - - +
1396M ALA* 3.8 22.7 - - + -
1397M LEU* 3.9 24.9 - - + -
1409M LEU* 5.1 7.9 - - + -
1412M ALA* 3.3 36.6 - - + +
1413M GLY* 4.0 0.2 - - - -
1416M ALA* 3.1 22.0 - - - +
1417M GLU* 2.9 22.0 + - + +
1418M LEU 5.2 0.2 - - - -
1419M ASP* 4.6 6.5 - - + -
1204N PHE* 5.8 1.1 - + - -
1207N LEU* 4.5 12.6 - - + -
1212N ILE* 4.6 10.1 - - + -
1213N THR* 3.3 2.2 - - - -
1214N PRO* 3.7 33.0 - - + -
1215N ARG* 6.0 0.2 - - - -
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Residues in contact with GLY 20 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19M PHE* 1.3 77.4 - - - +
21M LEU* 1.3 65.0 + - - +
228M PHE* 3.3 15.3 - - - -
229M SER* 4.3 0.7 - - - -
1413M GLY* 3.1 24.1 - - - -
1212N ILE* 3.6 2.1 - - - -
1213N THR* 3.0 35.4 + - - -
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Residues in contact with LEU 21 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20M GLY* 1.3 78.1 - - - +
22M PHE* 1.3 62.5 + - - +
23M SER 3.7 0.9 + - - -
26M GLU* 5.4 0.2 - - - +
95M PHE* 3.6 23.1 - - + -
224M PHE* 5.1 1.3 - - + -
228M PHE 2.8 14.4 + - - +
229M SER* 3.4 24.5 - - - -
230M ARG 4.8 1.3 - - - +
233M TRP* 3.6 32.3 - - + +
234M MET* 4.1 25.6 - - + +
1413M GLY* 3.1 31.0 - - - +
1414M ALA* 3.6 13.5 - - - +
1211N ASN* 3.7 5.8 - - - +
1212N ILE* 4.3 7.9 - - + -
1213N THR* 4.0 9.1 + - - +
1215N ARG* 4.6 5.4 + - - -
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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