Contacts of the strand formed by residues 121 - 127 (chain A) in PDB entry 1F15
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 VAL 121 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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117A PHE* 4.6 1.6 - - + -
119A SER* 4.5 4.3 - - - -
120A THR* 1.3 76.8 - - - +
122A TRP* 1.3 71.9 + - - +
123A VAL* 3.3 25.8 - - + -
152A VAL* 3.7 2.4 - - - +
153A TYR* 3.0 36.1 + - + +
187A VAL* 3.8 16.2 - - + -
188A TYR 3.6 5.2 - - - +
189A SER* 4.9 2.0 - - - +
194A LEU* 3.4 39.5 - - + -
199A LEU* 3.7 25.8 - - + -
201A LEU* 5.5 1.3 - - + -
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Residues in contact with TRP 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 THR* 3.9 11.2 - - - +
121A VAL* 1.3 80.5 - - - +
123A VAL* 1.3 64.1 + - - +
143A PHE* 3.6 24.0 - + + -
150A VAL* 3.9 25.1 - - + -
151A LEU 3.7 5.6 - - - -
152A VAL* 3.9 27.1 - - + +
187A VAL* 3.2 7.4 - - - -
188A TYR* 3.1 53.5 + + + -
190A LYS* 3.9 31.0 - - + +
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Residues in contact with VAL 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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109A ILE* 4.2 22.1 - - + +
111A VAL* 4.4 18.8 - - + -
121A VAL* 3.3 23.1 - - + -
122A TRP* 1.3 78.9 - - - +
124A THR* 1.3 73.7 + - - +
143A PHE* 4.5 0.2 - - - -
150A VAL* 3.0 16.7 - - - +
151A LEU* 2.9 31.2 + - + +
153A TYR* 5.6 1.6 - - + -
185A VAL* 4.3 3.4 - - + -
186A LEU 3.4 10.8 - - - +
187A VAL* 4.4 0.9 - - + -
201A LEU* 3.7 27.1 - - + -
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Residues in contact with THR 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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109A ILE* 5.0 7.0 - - - -
123A VAL* 1.3 79.6 + - - +
125A VAL* 1.3 86.3 + - - +
126A ARG* 4.9 0.9 - - - -
143A PHE* 3.5 21.0 - - - -
148A SER* 3.0 27.7 + - - +
149A PRO* 2.7 30.1 - - + +
150A VAL* 4.1 4.3 - - - +
168A TYR* 5.6 0.4 - - + -
184A ALA 4.5 0.2 - - - -
185A VAL* 3.4 5.5 - - - +
186A LEU* 3.1 35.0 + - - +
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Residues in contact with VAL 125 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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90A LEU* 4.4 9.0 - - + -
107A LEU* 4.0 23.8 - - + -
108A GLN 6.1 0.7 - - - -
109A ILE* 4.2 10.9 - - + +
124A THR* 1.3 89.1 - - - +
126A ARG* 1.3 68.4 + - - +
168A TYR* 3.0 32.8 + - + -
183A TYR* 4.1 21.3 - - + -
184A ALA 3.3 5.4 - - - +
185A VAL* 3.9 8.7 - - + -
203A VAL* 3.8 32.1 - - + -
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Residues in contact with ARG 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 THR* 4.6 0.9 - - + -
125A VAL* 1.3 75.2 - - - +
127A LYS* 1.3 66.7 - - - +
128A VAL* 2.9 7.6 + - - +
142A MET* 2.5 77.1 + - + +
143A PHE* 4.0 6.1 + - - +
145A ASP* 2.6 18.7 + - - -
146A GLY* 5.0 0.2 - - - -
147A ALA* 3.5 17.3 - - - +
148A SER* 2.7 44.1 + - - +
168A TYR* 3.7 6.1 - - - -
183A TYR* 3.5 7.0 - - - -
184A ALA* 2.7 37.3 + - - +
186A LEU* 4.5 14.8 - - + -
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Residues in contact with LYS 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 ARG* 1.3 75.9 - - - +
128A VAL* 1.3 58.1 + - - +
129A PRO* 2.9 22.4 - - + +
142A MET* 4.6 3.1 - - - +
168A TYR* 4.3 2.4 + - - +
182A LYS* 3.8 22.0 - - + -
183A TYR* 3.5 42.1 - - + +
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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