Contacts of the strand formed by residues 92 - 99 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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25E TRP* 4.9 6.7 - + + -
71E LEU* 4.2 7.4 - - + -
73E PHE* 3.6 39.3 - + - -
75E VAL* 5.1 2.2 - - + -
91E THR* 1.3 78.2 - - - +
93E ASN* 1.3 72.8 + - - +
117E THR* 3.7 1.0 - - - +
118E ILE* 2.7 72.3 + - + +
155E PHE* 4.1 27.8 - + + -
156E GLN 3.5 13.2 - - - +
157E ASP* 4.7 5.4 - - - +
158E ILE* 5.0 3.8 - - - -
162E VAL* 3.8 30.1 - - + -
164E LEU* 4.4 11.4 - - + -
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Residues in contact with ASN 93 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91E THR* 5.5 0.5 + - - -
92E PHE* 1.3 87.8 - - - +
94E LEU* 1.3 62.0 + - - +
95E TYR* 3.6 21.3 + - + -
114E LYS* 3.3 31.6 + - - +
116E ASP 3.8 1.8 - - - -
117E THR* 3.7 9.0 + - - +
154E ALA 3.8 0.2 - - - +
155E PHE* 3.4 7.8 - - - +
156E GLN* 2.7 54.9 + - + +
158E ILE* 4.0 19.9 - - - +
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Residues in contact with LEU 94 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69E ILE* 4.3 16.8 - - + -
71E LEU* 4.5 7.2 - - + -
93E ASN* 1.3 72.3 - - - +
95E TYR* 1.3 68.3 + - - +
114E LYS* 3.7 1.0 - - - +
115E ILE* 2.7 61.5 + - + -
116E ASP 3.1 17.0 + - - +
118E ILE* 3.9 16.4 - - + -
141E ARG* 4.1 23.3 - - + -
153E LEU* 4.4 11.9 - - + -
154E ALA 3.7 4.5 - - - +
155E PHE* 3.6 31.2 - - + -
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Residues in contact with TYR 95 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53E TRP* 3.7 37.6 - + + -
93E ASN* 3.6 30.4 + - + -
94E LEU* 1.3 81.1 - - - +
96E TYR* 1.3 64.6 + - - +
109E LYS 5.2 1.8 - - - -
112E PHE* 3.8 26.7 - - + -
113E THR 3.3 8.7 - - - -
114E LYS* 3.3 46.2 - - + +
115E ILE* 4.0 5.6 - - - +
153E LEU* 3.5 7.6 - - - +
154E ALA* 2.8 31.9 + - + +
156E GLN* 3.8 11.4 + - + -
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Residues in contact with TYR 96 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67E ILE* 6.3 1.6 - - + -
95E TYR* 1.3 78.1 - - - +
97E ALA* 1.3 68.7 + - - +
98E GLU* 3.9 19.1 + - + -
112E PHE* 3.4 8.2 - - - -
113E THR* 2.8 62.0 + - + +
114E LYS 5.1 0.2 - - - -
115E ILE* 3.5 29.2 - - + -
143E VAL* 3.4 28.9 - - + +
144E GLY* 6.0 0.5 - - - -
146E LEU* 3.9 21.8 - - + +
151E PHE* 5.2 3.6 - + + -
152E TYR 3.2 15.9 - - - +
153E LEU* 3.9 9.2 - - + -
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Residues in contact with ALA 97 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96E TYR* 1.3 81.0 - - - +
98E GLU* 1.3 66.5 + - - +
103E TYR* 5.8 4.5 - - + -
111E LEU* 3.5 24.0 - - + +
112E PHE* 3.7 27.3 - - + -
151E PHE* 3.2 3.3 - - - +
152E TYR* 2.8 36.3 + - + +
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Residues in contact with GLU 98 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61E ARG* 4.9 0.2 - - - -
96E TYR* 3.9 17.1 + - + -
97E ALA* 1.3 78.1 - - - +
99E SER* 1.3 66.0 + - - +
103E TYR* 5.0 2.8 + - - -
145E PRO 4.1 5.2 - - - +
146E LEU* 3.2 35.8 - - + +
147E THR* 2.8 30.7 + - - -
148E ARG* 3.2 25.4 + - + +
150E GLY 3.6 8.6 - - - +
151E PHE* 4.2 3.1 - - + +
152E TYR* 5.8 0.7 - - - -
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Residues in contact with SER 99 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58E TRP* 3.6 7.6 + - - -
97E ALA 4.3 0.2 + - - -
98E GLU* 1.3 78.8 - - - +
100E ASP* 1.3 62.0 + - - +
101E LEU* 2.5 35.3 + - - -
103E TYR* 3.7 28.8 - - - -
148E ARG* 3.7 11.0 - - - +
150E GLY* 2.9 35.2 + - - +
151E PHE* 4.6 0.6 - - - +
152E TYR* 4.3 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