Contacts of the strand formed by residues 147 - 155 (chain A) in PDB entry 1F6A
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 GLY 147 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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122A LYS* 5.5 0.2 - - - -
123A ASP* 3.5 14.8 - - - -
146A SER* 1.3 83.2 - - - +
148A THR* 1.3 65.7 + - - -
149A TYR* 3.6 8.4 - - - -
166A ASN* 4.4 1.1 - - - -
167A ILE 3.0 27.0 + - - +
3F FUC 4.6 17.4 - - - +
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Residues in contact with THR 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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121A TYR 4.5 0.2 - - - -
122A LYS* 3.6 1.6 - - - -
123A ASP* 2.8 39.3 + - - +
147A GLY* 1.3 75.0 - - - -
149A TYR* 1.3 63.7 + - - +
150A TYR* 5.1 5.5 - - - -
164A PRO* 4.9 8.2 - - - +
165A LEU 3.3 10.1 - - - -
166A ASN* 2.8 26.0 - - - +
1F NAG 3.9 22.2 - - - +
3F FUC 5.6 0.9 - - + +
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Residues in contact with TYR 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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90A LEU* 3.9 16.2 - - + -
103A LEU* 4.9 0.4 - - + +
105A LEU* 3.6 28.5 - - + -
120A TYR* 5.5 3.8 - + + -
121A TYR 3.0 17.9 - - - -
122A LYS* 3.5 27.0 + - + +
127A LEU* 3.5 26.8 - - + +
138A ILE* 4.2 8.4 - - + +
145A ASP* 2.8 36.0 + - - +
147A GLY 3.6 16.8 - - - -
148A THR* 1.3 75.5 - - - +
150A TYR* 1.3 64.2 + - - +
164A PRO* 3.4 1.6 - - - +
165A LEU* 2.6 44.2 + - - +
167A ILE* 3.7 26.5 - - + -
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Residues in contact with TYR 150 (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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90A LEU* 4.0 10.5 - - - +
120A TYR* 3.6 1.3 - - - +
121A TYR* 2.6 85.7 + + + -
124A GLY* 4.7 17.5 - - - -
148A THR* 5.1 6.7 - - - -
149A TYR* 1.3 84.0 - - - +
151A CYS* 1.3 60.6 + - - +
152A THR* 3.9 2.7 - - + -
161A GLU* 3.1 40.9 + - + -
162A SER* 3.7 10.3 - - - +
164A PRO* 3.8 23.6 - - + -
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Residues in contact with CYS 151 (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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88A LEU* 4.7 0.4 - - - +
89A LEU 4.6 0.7 - - - -
90A LEU* 4.0 12.3 - - + +
107A CYS* 2.1 51.4 - - + -
118A VAL* 4.6 0.7 - - + -
119A ILE 3.1 12.1 - - - +
120A TYR* 3.8 17.0 - - + -
150A TYR* 1.3 73.7 - - - +
152A THR* 1.3 66.9 + - - +
161A GLU* 3.4 3.3 - - - +
162A SER* 2.6 55.4 + - - -
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Residues in contact with THR 152 (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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88A LEU* 4.1 5.6 - - - -
117A LYS 4.4 0.7 + - - -
118A VAL* 3.2 6.1 - - - +
119A ILE* 2.8 39.9 + - - +
121A TYR* 3.6 29.9 + - + -
150A TYR* 3.9 4.9 - - + -
151A CYS* 1.3 80.1 - - - +
153A GLY* 1.3 59.0 + - - +
160A TYR 3.0 9.9 - - - -
161A GLU* 3.5 26.0 - - + -
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Residues in contact with GLY 153 (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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88A LEU* 3.7 5.0 - - - +
115A VAL* 3.8 14.8 - - - -
116A TYR 3.8 2.5 - - - -
117A LYS 3.6 13.0 - - - -
152A THR* 1.3 77.7 - - - +
154A LYS* 1.3 66.2 + - - -
158A LEU 3.7 0.3 - - - +
159A ASP* 3.6 2.8 - - - +
160A TYR* 2.8 35.0 + - - +
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Residues in contact with LYS 154 (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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114A ASP 4.0 0.2 - - - +
115A VAL* 3.2 5.2 - - - +
116A TYR* 2.7 45.1 + - - +
117A LYS* 4.2 33.8 - - + +
153A GLY* 1.3 74.5 - - - -
155A VAL* 1.3 60.4 + - - +
156A TRP 4.2 0.7 - - - -
157A GLN 4.5 13.2 + - - +
158A LEU 2.9 9.0 - - - +
159A ASP* 2.7 34.8 - - - +
371A CPS 4.1 25.7 + - - +
362B ASP* 5.7 0.4 + - - -
1G NAG 5.3 10.8 - - - +
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Residues in contact with VAL 155 (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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87A TRP* 4.1 16.7 - - + +
88A LEU* 4.2 10.5 - - + -
109A GLY* 5.7 0.4 - - - -
110A TRP 6.4 0.2 - - - +
113A TRP* 4.2 13.7 - - + -
114A ASP 3.7 13.7 - - - +
115A VAL* 3.0 33.2 - - + -
153A GLY 4.7 1.6 - - - +
154A LYS* 1.3 71.4 - - - +
156A TRP* 1.3 96.7 + - + +
157A GLN 3.4 0.2 + - - -
158A LEU* 3.0 14.1 + - - +
160A TYR* 3.9 27.3 + - + -
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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