Contacts of the strand formed by residues 131 - 136 (chain A) in PDB entry 1EFT
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 131 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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17A ILE* 4.5 19.7 - - + -
102A ALA* 3.7 11.7 - - + -
104A LEU* 4.1 14.8 - - + +
120A ILE* 4.6 11.4 - - + -
123A ALA* 5.1 4.0 - - + -
128A VAL* 4.8 2.5 - - + -
130A TYR* 1.3 81.7 - - - +
132A VAL* 1.3 73.2 + - - +
133A VAL* 4.4 6.1 - - + -
158A LEU* 3.8 31.0 - - + -
163A PHE* 3.8 36.8 - - + -
164A PRO* 6.3 0.6 - - - +
168A VAL* 3.6 16.8 - - + +
209A TYR* 3.6 18.1 + - - -
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Residues in contact with VAL 132 (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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102A ALA 3.1 10.4 + - - +
103A ILE* 3.4 4.6 - - + -
104A LEU 2.9 24.4 + - - -
131A ILE* 1.3 75.5 - - - +
133A VAL* 1.3 67.2 + - - +
169A PRO* 4.0 16.6 - - + +
171A ILE* 4.0 11.0 - - + -
202A LEU* 3.7 28.9 - - + -
205A ALA* 4.4 8.1 - - + +
206A ILE* 4.4 12.3 - - + -
209A TYR* 3.6 31.9 - - + -
210A ILE* 4.2 15.2 - - + +
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Residues in contact with VAL 133 (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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104A LEU* 3.4 19.7 - - + +
106A VAL* 4.2 9.9 - - + -
131A ILE* 4.4 2.2 - - + -
132A VAL* 1.3 78.1 - - - +
134A PHE* 1.3 68.4 + - - +
135A MET* 3.9 4.3 - - + +
154A VAL* 4.2 18.8 - - + -
158A LEU* 4.0 18.4 - - + -
168A VAL* 3.6 21.8 - - + -
169A PRO 3.0 11.8 + - - +
170A VAL* 3.5 23.6 - - + -
171A ILE* 3.0 31.1 + - - +
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Residues in contact with PHE 134 (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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27A LEU* 4.0 22.0 - - + -
103A ILE* 4.2 19.6 - - + +
104A LEU 2.9 10.7 + - - +
105A VAL* 3.5 5.6 - - + +
106A VAL 3.1 23.0 + - - -
132A VAL 4.2 0.4 + - - -
133A VAL* 1.3 74.3 - - - +
135A MET* 1.3 63.4 + - - +
136A ASN* 3.3 39.0 + - + -
171A ILE* 3.6 24.9 - - + -
173A GLY* 4.0 24.0 - - - -
174A SER 4.4 1.1 - - - -
175A ALA* 4.3 3.8 - - + -
198A LYS* 4.2 9.2 - - + -
199A ILE* 4.2 18.2 - - + -
202A LEU* 3.5 29.6 - - + -
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Residues in contact with MET 135 (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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106A VAL* 3.4 10.3 - - + +
108A ALA* 3.4 32.3 - - + -
133A VAL* 3.9 7.4 - - + +
134A PHE* 1.3 72.3 - - - +
136A ASN* 1.3 58.3 + - - +
138A VAL* 4.0 7.4 - - + +
147A LEU* 3.7 40.6 - - + +
150A VAL* 4.0 21.5 - - + -
151A GLU* 4.1 13.5 - - - -
154A VAL* 5.5 1.6 - - + -
170A VAL* 4.1 11.4 - - + -
171A ILE 2.8 15.7 + - - +
172A ARG* 3.4 19.3 - - + -
173A GLY 2.9 27.2 + - - +
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Residues in contact with ASN 136 (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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22A HIS 3.0 27.9 + - - +
23A GLY* 3.6 10.3 + - - -
105A VAL* 4.1 7.2 - - + -
106A VAL 2.8 11.0 + - - +
107A SER* 4.3 0.2 - - - -
108A ALA* 2.7 33.3 + - - +
134A PHE* 3.3 19.8 + - + -
135A MET* 1.3 72.3 - - - +
137A LYS* 1.3 72.9 + - - +
138A VAL 3.3 3.1 - - - -
173A GLY 3.5 1.8 - - - -
174A SER* 3.6 0.7 - - - -
175A ALA* 2.9 30.3 + - - +
406A GNP 3.0 28.9 + - - +
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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