Contacts of the strand formed by residues 144 - 149 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48A TYR* 5.6 0.7 - - - -
116A ARG* 3.4 45.3 + - - +
117A PHE 2.9 14.7 + - - +
118A ILE* 3.2 15.1 - - + +
119A GLU 2.9 25.1 + - - -
142A LYS 3.4 2.6 + - - -
143A THR* 1.3 73.7 - - - +
145A ILE* 1.3 75.9 + - - +
146A HIS* 5.3 3.8 - - + -
156A ALA* 5.1 1.3 - - + -
157A THR* 3.2 37.5 + - + +
158A LYS* 5.1 6.0 - - + -
160A ASP* 2.9 36.2 + - + +
162A THR* 4.2 5.2 - - - -
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Residues in contact with ILE 145 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119A GLU* 3.5 7.9 - - + +
131A TYR* 3.5 25.6 - - + +
134A LYS* 4.0 15.3 - - + -
135A ALA* 3.6 42.4 - - + +
138A ILE* 4.0 20.6 - - + -
143A THR 4.2 2.9 - - - +
144A HIS* 1.3 81.5 - - - +
146A HIS* 1.3 65.3 + - - +
147A ILE* 3.6 23.6 - - + -
156A ALA* 3.2 3.9 - - - +
157A THR* 2.8 38.6 + - - +
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Residues in contact with HIS 146 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48A TYR* 2.9 27.8 + + - +
118A ILE* 4.6 3.8 - - + -
119A GLU 3.0 7.3 + - - -
120A ILE* 3.4 19.0 - - + +
121A GLY 2.9 20.8 + - - +
144A HIS* 5.3 2.9 - - + -
145A ILE* 1.3 76.4 - - - +
147A ILE* 1.3 72.3 + - - +
148A PHE* 3.3 25.0 - + - -
154A GLU* 2.9 27.6 + - - -
155A MET 3.5 7.6 - - - -
156A ALA* 3.9 9.1 - - + +
160A ASP 5.2 0.2 + - - -
161A TYR* 3.3 32.2 + + - -
162A THR* 5.1 0.4 + - - -
168A ARG* 3.6 9.6 - - - -
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Residues in contact with ILE 147 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120A ILE 4.7 0.7 - - - -
121A GLY* 3.4 25.8 - - - +
123A THR* 3.8 13.5 - - + -
127A VAL* 4.4 9.9 - - + +
130A TYR* 3.7 30.7 - - + -
131A TYR* 3.8 36.1 - - + -
134A LYS* 4.7 5.4 - - + -
145A ILE* 3.6 19.5 - - + -
146A HIS* 1.3 75.2 - - - +
148A PHE* 1.3 74.4 + - - +
154A GLU* 3.2 9.1 - - - +
155A MET* 2.9 38.0 + - + +
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Residues in contact with PHE 148 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44A VAL* 4.1 18.6 - - + -
48A TYR* 3.9 25.4 - + - -
120A ILE* 4.3 2.7 - - + -
121A GLY 2.8 15.8 + - - +
122A VAL* 3.3 6.6 - - + -
123A THR* 2.9 28.6 + - - +
127A VAL* 4.7 0.2 - - - -
146A HIS* 3.3 33.9 - + - -
147A ILE* 1.3 78.3 - - - +
149A SER* 1.3 59.8 + - - +
153A GLU 3.7 6.1 - - - +
154A GLU* 3.6 28.7 - - + -
168A ARG* 4.3 13.0 - - + -
171A ILE* 3.9 31.0 - - + -
172A LYS* 4.5 11.9 - - + -
175A LEU* 3.9 16.8 - - + -
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Residues in contact with SER 149 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122A VAL* 5.2 0.2 - - - -
123A THR* 3.3 14.1 - - - -
124A ARG 6.1 0.2 - - - -
125A ARG 4.7 3.6 - - - -
127A VAL* 3.4 24.2 - - - -
148A PHE* 1.3 74.0 - - - +
150A PHE* 1.3 62.6 + - - +
151A THR* 2.7 33.1 + - - -
152A GLY* 3.4 9.2 + - - -
153A GLU* 3.0 18.3 + - - +
172A LYS* 5.6 1.6 - - - +
175A LEU* 3.6 17.0 - - - +
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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