Contacts of the strand formed by residues 92 - 99 (chain B) 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 PHE 92 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25B TRP* 5.0 6.1 - + + -
71B LEU* 4.2 8.1 - - + -
73B PHE* 3.6 39.0 - + - -
75B VAL* 5.1 2.0 - - + -
91B THR* 1.3 78.5 - - - +
93B ASN* 1.3 71.8 + - - +
117B THR* 3.9 0.5 - - - +
118B ILE* 2.7 74.5 + - + +
155B PHE* 4.0 28.3 - + + -
156B GLN 3.4 15.0 - - - +
157B ASP* 4.6 5.2 - - - -
158B ILE* 5.1 4.0 - - - -
162B VAL* 3.8 28.3 - - + -
164B LEU* 4.3 11.9 - - + -
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Residues in contact with ASN 93 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91B THR* 5.4 0.7 + - - -
92B PHE* 1.3 85.8 - - - +
94B LEU* 1.3 61.7 + - - +
95B TYR* 3.6 20.9 + - + -
114B LYS* 3.2 32.2 + - - +
116B ASP 3.8 1.6 - - - -
117B THR* 3.8 9.9 + - - +
155B PHE* 3.4 6.9 - - - -
156B GLN* 2.6 56.6 + - + +
158B ILE* 4.0 19.3 - - - +
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Residues in contact with LEU 94 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69B ILE* 4.3 16.4 - - + -
71B LEU* 4.5 6.7 - - + -
92B PHE 4.3 0.2 + - - -
93B ASN* 1.3 72.6 - - - +
95B TYR* 1.3 72.3 + - - +
114B LYS* 3.5 1.6 - - - +
115B ILE* 2.7 62.1 + - + -
116B ASP 3.1 16.6 + - - +
118B ILE* 4.0 15.0 - - + -
141B ARG* 4.1 22.4 - - + -
153B LEU* 4.5 11.0 - - + -
154B ALA 3.7 4.5 - - - +
155B PHE* 3.7 31.4 - - + -
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Residues in contact with TYR 95 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53B TRP* 3.7 33.8 - + + -
93B ASN* 3.6 29.8 + - + -
94B LEU* 1.3 80.6 - - - +
96B TYR* 1.3 59.7 + - - +
109B LYS 5.3 1.6 - - - -
112B PHE* 3.8 33.0 - - + -
113B THR 3.2 8.7 - - - -
114B LYS* 3.3 45.8 - - + +
115B ILE* 4.0 4.7 - - - +
153B LEU* 3.4 8.7 - - - +
154B ALA 2.7 35.6 + - - +
156B GLN* 3.8 13.2 + - + -
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Residues in contact with TYR 96 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67B ILE* 6.3 0.9 - - + -
95B TYR* 1.3 75.6 - - - +
97B ALA* 1.3 68.6 + - - +
98B GLU* 4.0 21.9 + - + -
112B PHE* 3.3 8.7 - - - -
113B THR* 2.8 63.6 + - + +
114B LYS 5.2 0.4 - - - -
115B ILE* 3.5 25.1 - - + -
143B VAL* 3.4 29.8 - - + +
144B GLY* 6.1 0.5 - - - -
146B LEU* 4.0 19.4 - - + +
151B PHE* 5.1 4.0 - + + -
152B TYR 3.1 16.4 - - - +
153B LEU* 3.8 13.2 - - + -
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Residues in contact with ALA 97 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96B TYR* 1.3 78.0 - - - +
98B GLU* 1.3 66.7 + - - +
103B TYR* 6.0 4.5 - - + -
111B LEU* 3.4 26.5 - - + +
112B PHE* 3.6 27.3 - - + -
151B PHE* 3.2 2.3 - - - +
152B TYR* 2.8 40.2 + - + +
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Residues in contact with GLU 98 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61B ARG* 4.9 0.2 - - - -
96B TYR* 4.0 17.7 + - + -
97B ALA* 1.3 77.7 - - - +
99B SER* 1.3 65.5 + - - +
103B TYR* 5.1 1.2 + - - -
145B PRO 4.3 4.5 - - - +
146B LEU* 3.3 33.2 - - + +
147B THR* 2.7 33.9 + - - -
148B ARG* 3.1 25.9 + - + +
150B GLY 3.5 10.3 - - - +
151B PHE* 4.4 3.6 - - + -
152B TYR* 5.8 0.7 - - - -
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Residues in contact with SER 99 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58B TRP* 3.7 7.6 + - - -
97B ALA 4.2 0.2 + - - -
98B GLU* 1.3 76.5 - - - +
100B ASP* 1.3 60.6 + - - +
101B LEU* 2.4 34.1 + - - -
103B TYR* 3.6 31.1 - - - -
148B ARG* 3.5 12.3 - - - +
150B GLY* 2.9 34.1 + - - +
151B PHE* 4.5 0.4 - - - +
152B TYR* 4.2 3.0 - - - -
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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