Contacts of the strand formed by residues 144 - 149 (chain C) in PDB entry 3HW4
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 HIS 144 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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48C TYR* 5.7 0.4 - - - -
116C ARG* 3.2 54.0 + - - +
117C PHE 2.7 11.9 + - - +
118C ILE* 3.1 11.7 - - + +
119C GLU 2.8 27.0 + - - +
142C LYS 3.3 4.2 + - - -
143C THR* 1.3 73.9 - - - +
145C ILE* 1.3 71.0 + - - +
146C HIS* 5.3 4.3 - - + -
156C ALA* 5.0 0.7 - - + -
157C THR* 3.1 42.8 + - + +
158C LYS* 4.9 4.9 - - + +
160C ASP* 2.8 35.2 + - + +
162C THR* 4.0 7.6 - - - -
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Residues in contact with ILE 145 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119C GLU* 3.5 11.7 - - + +
131C TYR* 3.5 26.9 - - + +
134C LYS* 4.1 11.0 - - + -
135C ALA* 3.6 41.7 - - + +
138C ILE* 3.8 24.0 - - + -
140C SER* 4.9 2.0 - - - +
143C THR 4.2 3.4 - - - +
144C HIS* 1.3 80.6 - - - +
146C HIS* 1.3 64.5 + - - +
147C ILE* 3.5 24.5 - - + -
156C ALA* 3.1 5.6 - - - +
157C THR* 2.7 45.8 + - - +
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Residues in contact with HIS 146 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48C TYR* 2.7 35.8 + + + +
118C ILE* 4.5 6.7 - - + -
119C GLU 3.0 8.9 + - - +
120C ILE* 3.3 9.1 - - + +
121C GLY 3.0 22.5 + - - +
144C HIS* 4.2 3.5 + - + -
145C ILE* 1.3 74.5 - - - +
147C ILE* 1.3 72.9 + - - +
148C PHE* 3.4 21.8 + + - -
154C GLU* 2.9 29.5 + - + -
155C MET 3.6 6.1 - - - -
156C ALA* 4.2 6.9 - - + +
160C ASP 5.0 0.2 + - - -
161C TYR* 3.2 35.8 + + - -
162C THR* 4.8 0.6 + - - -
168C ARG* 3.6 9.0 - - - -
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Residues in contact with ILE 147 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119C GLU 5.0 0.2 - - - +
121C GLY* 3.3 23.1 - - - +
123C THR* 3.7 28.9 - - + -
127C VAL* 3.8 17.0 - - + +
130C TYR* 3.8 17.9 - - + +
131C TYR* 3.6 30.1 - - + +
134C LYS* 4.8 4.0 - - + -
145C ILE* 3.5 22.9 - - + -
146C HIS* 1.3 78.3 - - - +
148C PHE* 1.3 65.6 + - - +
154C GLU* 3.0 10.0 - - - +
155C MET* 2.8 43.4 + - + +
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Residues in contact with PHE 148 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44C VAL* 4.0 22.2 - - + -
48C TYR* 3.9 24.0 - + - -
120C ILE* 4.4 6.7 - - + -
121C GLY 2.9 13.7 + - - +
122C VAL* 3.3 6.8 - - + -
123C THR* 3.0 27.2 + - - +
127C VAL* 4.1 3.6 - - - -
146C HIS* 3.4 27.8 - + - -
147C ILE* 1.3 73.9 - - - +
149C SER* 1.3 61.9 + - - +
153C GLU 3.6 4.3 - - - -
154C GLU* 3.6 27.4 - - + -
168C ARG* 3.9 14.6 - - + -
171C ILE* 3.9 31.0 - - + -
172C LYS* 4.3 14.4 - - + -
175C LEU* 3.7 17.9 - - + -
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Residues in contact with SER 149 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122C VAL* 5.2 0.2 - - - -
123C THR* 3.4 16.4 - - - -
124C ARG 5.8 0.2 - - - -
125C ARG 4.3 7.4 - - - -
127C VAL* 3.6 20.0 - - - -
148C PHE* 1.3 75.5 - - - +
150C PHE* 1.3 63.3 + - - +
151C THR* 2.6 30.9 + - - -
152C GLY* 3.9 6.2 + - - -
153C GLU* 3.0 24.0 + - - +
172C LYS* 5.5 1.9 - - - +
175C LEU* 3.4 20.4 - - - +
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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
------------------------------------------------------------
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