Contacts of the strand formed by residues 117 - 123 (chain D) in PDB entry 3HN3
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 THR 117 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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110D ARG* 3.5 24.0 + - - +
111D TRP* 3.9 14.8 - - + -
114D ASP* 2.9 21.5 + - - +
115D LEU 4.1 3.5 - - - +
116D ARG* 1.3 78.6 - - - +
118D ARG* 1.3 62.6 + - - +
119D VAL* 4.0 9.4 - - + -
154D SER* 4.0 2.6 + - - -
158D GLN* 2.9 30.3 + - - +
222D THR* 3.7 33.4 - - + -
223D THR 4.1 2.7 - - - +
225D THR* 4.5 2.7 - - - +
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Residues in contact with ARG 118 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116D ARG 3.7 1.2 + - - -
117D THR* 1.3 71.5 - - - +
119D VAL* 1.3 59.9 + - - +
120D VAL* 3.4 29.1 - - + +
150D GLU* 4.0 15.4 + - - -
152D ASP* 3.2 36.6 + - - +
154D SER* 3.4 4.7 - - - +
221D TYR* 3.8 3.3 + - - +
222D THR* 3.1 9.9 - - - -
223D THR* 2.9 68.0 + - - +
224D PRO 3.7 8.1 - - - +
225D THR* 4.2 11.9 - - + +
227D TYR* 3.4 52.2 + - - -
229D ASP* 5.0 2.2 + - - -
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Residues in contact with VAL 119 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107D LEU* 5.0 1.3 - - + -
111D TRP* 4.2 42.8 - - + +
117D THR* 4.0 18.2 - - + -
118D ARG* 1.3 75.7 - - - +
120D VAL* 1.3 61.8 + - - +
152D ASP* 3.4 5.9 - - - +
153D ILE* 2.8 54.9 + - + -
154D SER* 2.9 14.4 + - - +
157D VAL* 4.4 16.2 - - + -
158D GLN* 4.5 5.6 - - - +
220D LEU* 4.6 4.7 - - + -
221D TYR 3.6 5.8 - - - +
222D THR* 4.3 3.1 - - + -
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Residues in contact with VAL 120 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118D ARG* 3.4 42.0 - - + +
119D VAL* 1.3 79.4 - - - +
121D LEU* 1.3 63.4 + - - +
122D ARG 4.0 0.3 + - - -
150D GLU* 3.5 28.3 - - + +
151D ALA 3.4 12.6 - - - +
152D ASP* 4.7 2.2 - - - -
153D ILE* 4.8 0.2 - - - -
219D LEU 3.9 0.2 - - - +
220D LEU* 3.1 10.5 - - - +
221D TYR* 2.7 74.5 + - + +
223D THR* 5.2 0.2 - - + -
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Residues in contact with LEU 121 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41D LEU* 4.4 0.9 - - + -
119D VAL 4.4 0.2 + - - -
120D VAL* 1.3 73.0 - - - +
122D ARG* 1.3 59.4 + - - +
123D ILE* 4.2 11.4 + - + -
132D VAL* 3.9 19.1 - - + -
134D VAL* 4.4 10.3 - - + -
140D LEU* 4.4 5.5 - - + +
149D PHE 4.1 0.2 - - - +
150D GLU* 3.1 5.2 - - - +
151D ALA* 2.9 35.3 + - + +
153D ILE* 4.2 13.1 - - + +
168D ILE* 3.8 41.7 - - + -
218D VAL* 4.1 19.7 - - + -
219D LEU 3.6 15.9 - - - +
220D LEU* 3.7 19.5 - - + -
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Residues in contact with ARG 122 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27D MET* 3.5 29.5 + - - +
28D LEU 2.9 26.4 + - - +
29D TYR* 4.4 2.4 - - - +
30D PRO* 3.5 26.1 - - + +
120D VAL 4.0 0.4 + - - -
121D LEU* 1.3 72.9 - - - +
123D ILE* 1.3 75.5 + - - +
124D GLY* 4.6 2.2 - - - +
148D PRO* 4.2 9.4 - - - +
149D PHE 3.7 11.4 - - - -
150D GLU* 3.0 29.5 + - + +
218D VAL* 3.5 6.6 - - - +
219D LEU* 2.8 60.3 + - + +
221D TYR* 4.0 20.7 + - + -
390D GLU* 4.0 18.2 + - - -
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Residues in contact with ILE 123 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121D LEU* 4.2 16.6 - - + -
122D ARG* 1.3 76.9 - - - +
124D GLY* 1.3 64.7 + - - +
125D SER 3.3 23.4 + - - +
132D VAL* 4.7 6.3 - - + -
140D LEU* 4.8 2.7 - - + -
148D PRO* 3.3 1.2 - - - +
149D PHE* 2.8 68.4 + - + +
170D ILE* 3.6 24.9 - - + -
214D LEU* 3.9 16.2 - - + -
217D SER 4.4 0.9 - - - -
218D VAL* 3.3 31.4 - - + -
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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