Contacts of the strand formed by residues 121 - 126 (chain E) in PDB entry 2F53
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 GLU 121 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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119E PRO* 5.1 3.4 - - + +
120E PRO* 1.3 75.0 - - - +
122E VAL* 1.3 60.5 + - - +
143E LEU 3.7 0.3 - - - +
144E ALA* 3.4 4.2 - - - -
145E THR* 2.9 47.2 + - - +
184E ARG* 5.7 5.9 + - - +
232E VAL* 4.5 2.2 - - - -
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Residues in contact with VAL 122 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133D LYS* 5.6 0.2 + - - -
120E PRO* 4.6 3.4 - - + -
121E GLU* 1.3 80.5 - - - +
123E ALA* 1.3 66.8 + - - +
142E CYS* 3.5 28.3 - - - -
143E LEU 3.5 3.1 - - - +
144E ALA* 4.4 5.2 - - + -
207E CYS* 4.2 7.6 - - - +
209E VAL* 3.8 18.2 - - + -
232E VAL* 3.6 39.8 - - + +
233E SER 4.3 5.9 - - - +
234E ALA* 3.6 26.7 - - + +
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Residues in contact with ALA 123 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127D ASP* 4.2 12.1 - - - +
133D LYS* 3.9 23.6 - - - +
122E VAL* 1.3 78.2 - - - +
124E VAL* 1.3 63.1 + - - +
125E PHE* 3.8 22.0 - - + -
141E VAL 3.8 0.9 - - - +
142E CYS* 3.3 4.0 - - - -
143E LEU* 2.9 33.9 + - + +
234E ALA* 3.7 4.5 - - - -
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Residues in contact with VAL 124 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127D ASP* 3.2 7.2 + - - +
128D SER* 3.0 32.5 + - - +
123E ALA* 1.3 74.7 - - - +
125E PHE* 1.3 70.3 + - - +
126E GLU 4.1 0.2 - - - -
140E LEU* 4.2 15.7 - - + -
141E VAL 3.4 6.3 - - - +
142E CYS* 4.5 1.3 - - - -
156E TRP* 4.5 9.2 - - + -
205E PHE 5.5 0.9 - - - +
206E ARG* 5.4 0.2 - - - -
207E CYS* 3.7 22.4 - - + +
234E ALA* 3.5 38.0 - - + +
235E GLU* 4.1 4.5 - - - +
236E ALA* 4.0 23.1 - - + +
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Residues in contact with PHE 125 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125D LEU* 3.5 19.9 - - + +
126D ARG 3.3 4.7 - - - +
127D ASP* 3.5 27.4 - - + -
133D LYS* 4.0 13.0 - - + -
134D SER* 3.8 27.4 - - - -
135D VAL* 3.8 33.4 - - + -
123E ALA* 3.8 31.9 - - + -
124E VAL* 1.3 75.8 - - - +
126E GLU* 1.3 63.3 + - - +
140E LEU* 3.5 8.3 - - - +
141E VAL* 2.7 45.9 + - + +
143E LEU* 3.9 23.1 - - + -
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Residues in contact with GLU 126 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125D LEU* 3.2 24.2 - - - +
126D ARG* 2.8 18.3 + - + +
127D ASP 5.4 0.2 - - - -
128D SER* 3.2 40.1 - - - +
124E VAL* 5.5 0.2 - - - -
125E PHE* 1.3 72.1 - - - +
127E PRO* 1.3 78.1 - - + +
128E SER* 4.5 0.2 - - - -
140E LEU* 5.2 0.9 - - - -
198E TRP* 3.8 22.1 - - + -
236E ALA* 4.2 7.2 - - + +
237E TRP 4.6 3.5 + - - +
239E ARG* 3.1 36.6 + - - -
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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