Contacts of the strand formed by residues 16 - 21 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14A VAL* 3.5 7.2 - - - +
15A LYS* 1.3 82.9 - - - +
17A VAL* 1.3 65.0 - - - +
18A GLN 4.1 0.4 - - - -
1418A LEU* 4.1 21.4 - - + +
1419A ASP 3.1 12.6 - - - +
1420A ASP* 5.3 1.9 - - - +
1421A CYS* 4.0 0.4 - - - -
1215B ARG 4.0 0.3 - - - +
1217B TYR* 3.1 30.0 + - + +
1219B ASP 3.6 2.0 - - - +
1220B ARG* 3.5 31.0 + - + +
1221B SER* 3.0 26.0 + - - -
1222B ARG* 3.3 17.5 + - - +
13D ARG* 2.7 31.7 + - - -
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Residues in contact with VAL 17 (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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14A VAL* 4.0 9.6 - - + -
16A GLU* 1.3 80.3 - - - +
18A GLN* 1.3 58.2 + - - +
19A PHE* 3.5 35.4 + - + -
1397A LEU* 4.1 17.5 - - + -
1417A GLU 3.8 0.2 - - - +
1418A LEU* 3.5 8.0 - - - -
1419A ASP* 2.9 37.2 + - + -
1421A CYS* 3.5 21.1 - - - -
1430A LEU* 4.7 2.9 - - + -
1204B PHE* 5.7 2.0 - - + -
1214B PRO* 4.6 8.1 - - + -
1215B ARG 3.2 12.3 - - - +
1216B LEU* 4.3 14.4 - - + -
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Residues in contact with GLN 18 (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 GLU 4.1 1.2 - - - -
17A VAL* 1.3 71.8 - - - +
19A PHE* 1.3 86.8 + - - +
228A PHE* 3.6 42.4 - - + -
1416A ALA 3.7 12.0 + - - +
1417A GLU 3.4 3.4 + - - +
1418A LEU* 3.4 29.9 - - + +
1213B THR 3.2 0.7 - - - +
1214B PRO 4.7 0.4 - - - -
1215B ARG* 2.9 56.1 + - + +
1217B TYR* 3.8 15.2 - - + -
12D ARG* 5.2 2.4 - - - +
13D ARG* 4.4 6.5 - - - +
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Residues in contact with PHE 19 (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 VAL* 3.5 33.0 - - + -
18A GLN* 1.3 89.1 - - - +
20A GLY* 1.3 58.4 + - - +
228A PHE* 4.0 2.4 - - - +
1396A ALA* 3.9 21.3 - - + -
1397A LEU* 3.9 25.4 - - + -
1409A LEU* 4.8 7.6 - - + -
1412A ALA* 3.3 37.5 - - + +
1413A GLY* 3.9 0.9 - - - -
1416A ALA* 3.1 17.5 - - - +
1417A GLU* 3.0 19.3 + - + +
1418A LEU 5.1 0.4 - - - -
1419A ASP* 4.5 6.3 - - + -
1204B PHE* 6.2 0.4 - + - -
1207B LEU* 4.4 13.7 - - + -
1212B ILE* 4.6 10.5 - - + -
1213B THR* 3.3 5.4 - - - -
1214B PRO* 4.1 26.0 - - + -
1215B ARG* 5.5 0.2 - - - -
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Residues in contact with GLY 20 (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* 1.3 77.6 - - - +
21A LEU* 1.3 66.5 + - - +
228A PHE* 3.2 15.5 - - - -
229A SER* 4.3 0.4 - - - -
1413A GLY* 3.1 23.4 - - - -
1212B ILE* 3.6 1.4 - - - -
1213B THR* 2.9 35.6 + - - -
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Residues in contact with LEU 21 (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 GLY* 1.3 80.1 - - - +
22A PHE* 1.3 62.3 + - - +
23A SER 3.6 2.3 + - - -
26A GLU* 5.0 0.2 - - - +
95A PHE* 3.7 23.8 - - + -
224A PHE* 5.2 2.2 - - + -
228A PHE 2.7 16.8 + - - +
229A SER* 3.6 19.1 - - - -
230A ARG 5.0 0.9 - - - +
233A TRP* 3.7 32.1 - - + +
234A MET* 4.0 25.8 - - + +
1413A GLY* 3.1 29.8 - - - +
1414A ALA* 3.7 12.6 - - - +
1211B ASN* 3.7 9.2 - - - +
1212B ILE* 4.2 9.4 - - + -
1213B THR* 4.0 8.9 + - - +
1215B ARG* 4.5 5.7 + - - -
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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