Contacts of the strand formed by residues 147 - 153 (chain D) in PDB entry 1EFP
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 ALA 147 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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144D ALA 4.4 1.6 - - - +
145D THR 3.2 1.9 - - - -
146D PHE* 1.3 75.2 - - - +
148D SER* 1.3 59.7 + - - +
150D VAL* 4.1 10.3 - - + -
159D VAL* 3.4 26.7 - - + -
160D THR 3.8 5.2 - - - -
178D VAL* 3.8 17.3 - - + -
179D THR 3.0 16.3 + - - +
181D ASP* 3.3 21.1 + - - +
184D LEU* 3.3 15.1 - - + +
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Residues in contact with SER 148 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146D PHE 3.6 2.2 + - - -
147D ALA* 1.3 71.3 - - - +
149D LYS* 1.3 62.0 + - - +
160D THR* 2.8 21.5 + - - -
161D ARG 5.0 0.4 - - - -
162D GLU* 2.7 28.9 + - - +
167D LEU* 5.0 2.2 - - - -
181D ASP* 4.9 1.3 + - - -
183D ARG* 3.8 27.9 + - - +
184D LEU* 3.3 30.2 - - - +
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Residues in contact with LYS 149 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147D ALA 3.7 0.2 - - - -
148D SER* 1.3 80.0 - - - +
150D VAL* 1.3 65.9 + - - +
151D GLU* 3.5 41.5 + - + +
159D VAL* 3.2 9.9 - - - +
160D THR* 3.1 42.4 + - + +
184D LEU* 3.8 4.2 - - - +
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Residues in contact with VAL 150 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45D GLU* 4.0 22.3 + - + +
49D LEU* 4.9 9.3 - - + +
52D LYS* 4.8 8.7 + - - -
116D LEU* 5.8 4.0 - - + -
118D ILE* 6.2 2.9 - - + -
147D ALA* 4.1 17.0 - - + -
149D LYS* 1.3 80.0 - - - +
151D GLU* 1.3 60.2 + - - +
152D ILE* 3.4 23.1 + - + +
157D ALA* 4.6 11.0 - - + -
158D LYS 3.9 2.2 - - - -
159D VAL* 4.5 7.4 - - + +
178D VAL* 4.4 20.9 - - + -
184D LEU* 4.1 22.4 - - + +
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Residues in contact with GLU 151 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52D LYS* 5.9 1.8 - - - +
149D LYS* 3.5 37.1 + - + +
150D VAL* 1.3 70.0 - - - +
152D ILE* 1.3 64.3 + - - +
153D GLU* 3.4 13.7 + - - +
157D ALA* 4.4 0.4 - - - -
158D LYS* 2.9 67.2 + - + +
160D THR* 4.7 6.4 - - - +
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Residues in contact with ILE 152 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1D MET* 3.3 32.3 - - + -
49D LEU* 3.8 26.5 - - + -
52D LYS* 4.9 2.3 + - - +
54D GLN* 3.6 35.2 + - + +
116D LEU* 3.8 22.0 - - + -
150D VAL* 3.4 9.2 + - + +
151D GLU* 1.3 74.1 - - - +
153D GLU* 1.3 62.9 + - - +
154D GLY 4.9 3.1 - - - +
157D ALA* 3.7 13.2 - - + -
174D LEU* 3.5 29.8 - - + -
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Residues in contact with GLU 153 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54D GLN* 5.7 1.3 - - - +
151D GLU* 3.9 15.5 - - - +
152D ILE* 1.3 75.0 - - - +
154D GLY* 1.3 62.0 + - - +
155D ALA 3.7 0.3 + - - -
156D LYS* 2.8 45.9 + - + +
157D ALA* 5.2 1.1 - - - -
158D LYS* 4.2 22.9 - - + +
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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