Contacts of the strand formed by residues 125 - 129 (chain A) in PDB entry 2CFZ
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 125 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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116A GLN* 3.3 3.2 - - - -
117A VAL* 2.8 55.6 + - + +
124A ASN* 1.3 74.8 - - - +
126A THR* 1.3 63.6 + - - +
127A PHE* 3.7 26.7 - - + -
136A VAL* 3.8 11.4 - - + -
137A VAL 3.9 2.5 - - - -
138A ASP 3.2 24.9 - - - +
139A THR* 4.1 8.5 - - - -
140A LEU* 3.9 17.7 - - + -
146A ALA* 4.7 2.7 - - + -
149A ALA* 3.6 19.5 - - + -
181A LEU* 4.0 18.6 - - + -
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Residues in contact with THR 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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114A ILE* 4.2 2.7 - - + -
115A TYR 3.4 13.2 - - - +
116A GLN* 2.9 23.8 + - + +
124A ASN* 4.9 1.6 + - - +
125A ILE* 1.3 75.0 + - - +
127A PHE* 1.3 62.9 + - - +
128A ILE* 4.0 23.6 - - + -
136A VAL* 3.3 9.7 - - - +
137A VAL* 3.0 46.1 + - - +
296A LEU* 4.6 8.3 - - + +
341A PHE* 3.8 24.4 - - + -
342A ALA 5.0 0.2 + - - -
343A VAL* 5.8 2.9 - - - +
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Residues in contact with PHE 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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114A ILE* 3.6 2.1 - - - -
115A TYR* 2.8 51.8 + - + +
117A VAL* 4.6 5.2 - - + -
125A ILE* 3.7 46.4 - - + -
126A THR* 1.3 75.9 - - - +
128A ILE* 1.3 63.2 + - - +
134A TRP* 3.7 39.5 - + + -
135A ILE 3.7 2.0 - - - -
136A VAL* 3.6 19.1 - - + -
149A ALA 4.7 1.1 - - - -
150A TYR* 3.8 42.4 - + + -
153A VAL* 3.8 25.1 - - + -
162A ILE* 4.4 1.6 - - + -
181A LEU* 4.9 1.8 - - + -
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Residues in contact with ILE 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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113A GLY 3.4 7.9 - - - +
114A ILE* 4.4 11.4 - - + -
126A THR* 4.0 14.4 - - + -
127A PHE* 1.3 76.8 - - - +
129A ARG* 1.3 66.9 + - - +
130A GLY 3.3 0.3 + - - -
134A TRP* 3.5 4.5 - - - -
135A ILE* 2.8 48.3 + - + +
137A VAL* 3.9 21.3 - - + -
269A VAL* 4.3 17.0 - - + -
271A PHE* 3.8 38.1 - - + -
287A ILE* 5.7 0.4 - - + -
289A LEU* 4.0 17.7 - - + -
292A GLN* 4.5 9.6 - - - +
296A LEU* 5.3 2.7 - - + -
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Residues in contact with ARG 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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112A GLU* 5.5 4.6 + - - -
113A GLY* 2.8 31.2 + - - +
115A TYR* 4.8 5.4 - - + -
128A ILE* 1.3 70.4 - - - +
130A GLY* 1.3 59.9 + - - +
134A TRP* 3.7 20.6 - - + -
160A ARG* 2.7 43.0 - - - +
269A VAL* 3.4 17.5 - - - +
291A ARG* 4.0 9.5 + - - +
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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