Contacts of the strand formed by residues 150 - 157 (chain D) in PDB entry 3HPN
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 GLY 150 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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58D TRP* 3.4 20.1 - - - -
59D VAL 3.1 13.9 - - - -
60D TYR* 4.1 0.2 - - - -
61D ARG* 3.9 3.1 - - - -
98D GLU* 3.5 4.3 - - - +
99D SER 2.9 27.2 + - - +
148D ARG* 3.2 6.7 - - - +
149D LYS* 1.3 80.9 - - - +
151D PHE* 1.3 66.5 + - - +
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Residues in contact with PHE 151 (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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4D LEU* 4.0 16.4 - - + -
5D LEU* 6.4 0.2 - - + -
58D TRP* 3.4 5.8 - - - +
59D VAL* 2.8 73.7 + - + +
60D TYR 4.0 3.4 - - - -
61D ARG* 4.4 9.0 - - + -
67D ILE* 3.5 25.6 - - + -
96D TYR* 5.1 3.6 - + + -
97D ALA 3.3 13.2 - - - +
98D GLU* 4.2 13.5 - - + +
99D SER 4.6 0.4 - - - +
146D LEU* 3.8 24.7 - - + -
150D GLY* 1.3 77.6 - - - +
152D TYR* 1.3 68.6 + - - +
153D LEU* 3.9 23.1 - - + -
169D VAL* 4.0 13.7 - - + -
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Residues in contact with TYR 152 (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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55D ARG* 3.5 34.8 - - + -
56D THR* 3.4 20.6 - - - -
57D ASN 3.8 4.9 - - - -
58D TRP* 3.4 36.1 - + - -
96D TYR* 3.1 9.4 - - - +
97D ALA* 2.8 37.4 + - + +
98D GLU 5.7 0.2 - - - -
99D SER* 4.2 5.8 - - - -
102D ASP* 2.7 28.0 + - - -
103D TYR* 2.9 40.5 + + - +
104D GLY 4.0 1.2 + - - -
112D PHE* 3.8 24.0 - + + -
151D PHE* 1.3 76.1 - - - +
153D LEU* 1.3 65.2 + - - +
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Residues in contact with LEU 153 (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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5D LEU* 5.3 0.9 - - + -
55D ARG* 3.5 4.0 - - - +
56D THR* 3.0 46.9 + - + +
67D ILE* 4.5 3.1 - - + -
69D ILE* 3.8 39.3 - - + -
94D LEU* 4.4 7.6 - - + -
95D TYR 3.4 7.6 - - - +
96D TYR* 3.9 14.4 - - + -
112D PHE* 4.4 0.9 - - - -
151D PHE* 3.9 21.9 - - + -
152D TYR* 1.3 80.1 - - - +
154D ALA* 1.3 61.2 + - - +
155D PHE* 4.6 5.8 - - + -
167D VAL* 4.6 10.5 - - + -
169D VAL* 3.6 29.2 - - + -
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Residues in contact with ALA 154 (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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53D TRP* 3.9 20.9 - - + -
54D LEU 3.0 10.8 - - - +
55D ARG* 4.3 2.5 - - + -
94D LEU* 3.7 4.9 - - - +
95D TYR* 2.9 34.7 + - + +
107D PHE* 4.3 7.0 - - + -
112D PHE* 3.6 27.6 - - + -
153D LEU* 1.3 76.4 - - - +
155D PHE* 1.3 68.2 + - - +
156D GLN 4.2 0.2 - - - -
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Residues in contact with PHE 155 (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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16D TRP* 3.8 21.1 - + - -
25D TRP* 3.3 21.8 + - + -
52D ASN 3.2 1.9 - - - +
53D TRP* 3.2 7.7 - - - -
54D LEU* 2.6 59.5 + - + +
56D THR* 4.2 12.3 - - + -
71D LEU* 3.6 24.5 - - + -
92D PHE* 4.1 17.0 - + + -
93D ASN 3.5 5.4 - - - +
94D LEU* 3.7 22.0 - - + -
153D LEU* 4.8 4.7 - - + -
154D ALA* 1.3 80.3 - - - +
156D GLN* 1.3 60.8 + - - +
164D LEU* 3.9 14.8 - - + -
167D VAL* 4.0 26.5 - - + -
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Residues in contact with GLN 156 (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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25D TRP* 4.4 2.2 - - - -
51D ASP* 2.7 32.6 + - - +
52D ASN 3.2 3.8 - - - +
53D TRP* 3.7 34.0 - - + +
92D PHE* 3.5 7.4 - - - +
93D ASN* 2.8 68.7 + - + +
95D TYR* 3.7 12.7 + - + -
154D ALA 4.2 0.4 - - - -
155D PHE* 1.3 71.4 - - - +
157D ASP* 1.3 69.9 + - - +
158D ILE* 3.9 13.6 + - - +
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Residues in contact with ASP 157 (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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25D TRP* 3.7 28.7 - - + +
42D VAL* 3.3 24.5 - - + +
44D ASN* 5.1 1.4 - - - +
50D GLN* 3.6 1.7 - - - +
51D ASP* 3.4 6.9 + - - -
52D ASN* 2.6 60.1 + - + +
91D THR 5.1 0.2 - - - +
92D PHE* 4.7 3.8 - - + -
156D GLN* 1.3 74.4 - - - +
158D ILE* 1.3 57.1 + - - +
159D GLY* 2.9 25.8 + - - -
160D ALA* 2.9 21.6 + - - +
162D VAL* 4.8 1.7 - - + +
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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