Contacts of the strand formed by residues 151 - 156 (chain F) in PDB entry 2HEY
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 LYS 151 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91F ASN* 6.0 2.0 - - - +
93F SER* 3.7 22.9 - - - +
94F VAL 3.4 6.5 - - - +
95F VAL* 4.7 19.5 - - + -
120F PHE 2.8 25.6 + - - +
121F ARG* 3.5 2.1 + - - +
122F GLU* 4.0 31.6 + - - +
149F LYS* 3.7 10.5 + - - +
150F ASP* 1.3 79.9 - - - +
152F VAL* 1.3 61.3 + - - +
153F TYR* 3.3 17.6 - - + -
191F SER* 6.2 2.2 - - - -
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Residues in contact with VAL 152 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77F ILE* 4.3 2.8 - - - +
93F SER* 3.2 3.6 - - - -
94F VAL* 2.8 47.5 + - + +
96F ILE* 4.1 26.0 - - + -
104F ILE* 4.3 14.4 - - + -
118F LEU* 3.8 25.1 - - + -
119F HIS 3.3 4.5 - - - +
120F PHE* 4.3 12.6 - - + -
146F LEU* 4.1 16.6 - - + -
150F ASP* 5.6 0.2 - - + -
151F LYS* 1.3 71.7 - - - +
153F TYR* 1.3 63.5 + - - +
154F LEU* 5.9 0.2 - - + -
173F LEU* 5.0 6.3 - - + -
175F VAL* 4.4 14.6 - - + -
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Residues in contact with TYR 153 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74F GLN* 3.8 28.5 - - - +
77F ILE* 4.7 3.6 - - - -
92F ASN 3.6 20.9 - - - +
93F SER* 3.9 9.4 - - - -
118F LEU* 3.7 2.1 - - - +
119F HIS* 2.9 70.3 + + + +
121F ARG* 3.5 13.2 + - - -
122F GLU* 3.5 34.7 + - + +
151F LYS* 3.3 20.2 - - + -
152F VAL* 1.3 75.8 - - - +
154F LEU* 1.3 70.2 + - - +
155F THR* 4.1 8.3 - - + -
119R TYR* 5.4 0.3 + - - -
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Residues in contact with LEU 154 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67F VAL* 5.4 2.0 - - + -
74F GLN* 3.1 10.5 - - - +
75F LEU* 3.0 56.4 + - + +
77F ILE* 4.8 9.3 - - + +
92F ASN 5.2 0.2 + - - -
106F LEU* 3.8 25.4 - - + -
116F ILE* 4.0 5.2 - - + -
117F ASP 3.3 7.0 - - - +
118F LEU* 3.8 21.3 - - + -
129F ILE* 3.7 29.8 - - + -
152F VAL* 5.9 0.4 - - + -
153F TYR* 1.3 80.1 - - - +
155F THR* 1.3 61.8 + - - +
173F LEU* 4.2 25.8 - - + -
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Residues in contact with THR 155 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73F GLY 3.3 12.6 - - - +
74F GLN* 4.1 13.9 - - + +
116F ILE* 3.3 8.9 - - - +
117F ASP* 2.9 41.7 + - - +
119F HIS* 2.7 36.3 + - + +
153F TYR* 4.1 9.9 - - + -
154F LEU* 1.3 75.8 - - - +
156F VAL* 1.3 66.5 + - - +
157F ASN 5.2 0.2 + - - -
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Residues in contact with VAL 156 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70F CYS* 3.9 23.1 - - - -
73F GLY* 2.9 19.3 + - - +
75F LEU* 3.8 31.6 - - + +
114F VAL* 5.0 9.0 - - + -
115F LYS 3.5 9.0 - - - +
116F ILE* 4.6 5.8 - - + -
155F THR* 1.3 79.3 - - - +
157F ASN* 1.3 59.5 + - - +
158F ALA* 3.2 29.5 + - + +
162F LEU* 4.2 14.8 - - + -
163F CYS* 5.3 2.7 - - + -
166F LEU* 4.4 10.3 - - + -
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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