Contacts of the strand formed by residues 119 - 129 (chain A) in PDB entry 1F4L
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 ILE 119 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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110A TYR* 3.8 35.7 - - + +
113A LEU* 3.8 13.3 + - + -
114A LYS* 3.7 39.7 - - + +
117A GLY* 3.4 3.1 - - - +
118A PHE* 1.3 86.7 - - - +
120A LYS* 1.3 73.5 + - - +
121A ASN* 4.7 3.6 + - - +
190A PHE* 4.0 19.3 - - + -
191A PHE 3.4 9.2 - - - +
192A PHE* 4.1 8.1 - - + -
231A ILE* 3.9 24.0 - - + -
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Residues in contact with LYS 120 (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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117A GLY* 3.0 25.4 + - - -
118A PHE 4.2 1.6 - - - -
119A ILE* 1.3 95.7 - - - +
121A ASN* 1.3 67.7 + - - +
122A ARG* 6.1 0.9 - - + -
190A PHE* 3.4 4.9 - - - -
191A PHE* 2.7 46.1 + - + +
193A ASP* 4.4 10.9 + - + +
228A GLN* 3.0 42.6 - - - +
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Residues in contact with ASN 121 (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 LYS* 5.8 3.4 - - - +
119A ILE* 4.7 4.4 + - - +
120A LYS* 1.3 79.0 - - - +
122A ARG* 1.3 63.4 + - - +
188A GLU* 4.5 20.2 - - + +
189A HIS 3.4 6.7 - - - +
190A PHE* 3.1 37.2 - - - -
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Residues in contact with ARG 122 (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 LYS* 6.1 1.1 - - + -
121A ASN* 1.3 77.4 - - - +
123A THR* 1.3 72.8 + - - +
124A ILE* 3.6 18.2 + - - +
188A GLU* 4.5 2.9 - - - +
189A HIS* 2.9 34.5 + - - +
191A PHE* 3.3 45.9 - - + -
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Residues in contact with THR 123 (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 ARG* 1.3 87.2 + - - +
124A ILE* 1.3 70.4 + - - +
186A ASP* 3.8 35.2 - - + +
187A SER 3.5 10.5 - - - +
188A GLU* 4.2 11.7 - - - +
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Residues in contact with ILE 124 (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 ARG* 3.6 30.7 - - - +
123A THR* 1.3 84.5 - - - +
125A SER* 1.3 68.9 + - - +
126A GLN* 4.3 12.1 + - + +
185A ARG 3.9 0.2 - - - +
186A ASP* 3.3 4.0 - - - -
187A SER* 2.9 29.4 + - - +
189A HIS* 3.5 41.7 - - + +
191A PHE* 4.0 12.6 - - + -
230A ASP* 3.8 13.2 - - - +
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Residues in contact with SER 125 (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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124A ILE* 1.3 80.0 - - - +
126A GLN* 1.3 62.6 + - - +
184A MET* 3.1 26.9 - - - +
185A ARG 3.4 7.9 - - - -
186A ASP* 3.7 16.8 - - - -
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Residues in contact with GLN 126 (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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124A ILE* 4.2 12.6 - - + +
125A SER* 1.3 76.1 + - - +
127A LEU* 1.3 75.0 + - - +
135A PHE* 3.4 34.2 - - + +
136A LEU 3.1 31.8 + - - +
137A PRO* 4.0 5.5 - - - +
184A MET* 3.8 10.0 - - - +
185A ARG 3.0 26.2 + - - +
187A SER* 6.4 0.4 - - - -
189A HIS* 4.3 18.4 + - - -
233A ARG* 6.0 3.0 - - - +
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Residues in contact with LEU 127 (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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126A GLN* 1.3 82.5 - - - +
128A TYR* 1.3 57.4 + - - +
135A PHE* 3.5 2.3 - - - -
136A LEU* 2.9 29.3 + - + +
141A VAL* 3.9 33.4 - - + -
167A PRO* 4.0 32.5 - - + +
168A THR* 4.2 10.5 - - + +
173A PRO* 5.6 5.4 - - + -
182A PRO* 4.0 32.3 - - + +
183A VAL 3.5 7.4 - - - -
184A MET* 3.5 25.2 - - + +
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Residues in contact with TYR 128 (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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127A LEU* 1.3 74.4 - - - +
129A ASP* 1.3 64.8 + - - +
130A PRO* 3.3 30.4 + - + +
133A GLY* 3.6 15.8 + - - -
134A MET* 3.6 30.3 - - - -
135A PHE* 3.7 18.2 - + + -
136A LEU* 4.5 1.6 - - - +
182A PRO* 3.2 8.1 - - - +
183A VAL* 2.8 44.2 + - + +
185A ARG* 3.5 56.6 + - + -
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Residues in contact with ASP 129 (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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128A TYR* 1.3 73.5 - - - +
130A PRO* 1.3 58.9 - - - +
131A GLU* 3.0 8.3 + - - +
132A LYS* 3.0 30.1 + - + +
133A GLY* 2.7 29.3 + - - -
134A MET* 2.8 23.9 + - + +
136A LEU* 4.2 10.7 - - + +
175A SER* 2.5 35.5 + - - +
177A VAL* 4.3 1.4 - - - +
178A SER* 2.7 24.1 + - - -
180A ALA* 3.7 2.2 - - - +
182A PRO* 4.7 1.8 - - - -
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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