Contacts of the strand formed by residues 156 - 163 (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 LYS 156 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152D ILE* 3.8 1.4 - - - +
153D GLU* 2.8 51.7 + - + +
154D GLY 3.1 3.0 + - - +
155D ALA* 1.3 82.1 - - - +
157D ALA* 1.3 63.7 + - - +
158D LYS* 6.2 3.4 - - + -
171D ALA* 4.8 18.5 - - + +
172D VAL 3.0 19.7 - - - +
173D SER* 4.2 2.0 - - - -
174D LEU* 3.7 8.2 - - - +
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Residues in contact with ALA 157 (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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116D LEU* 6.2 2.5 - - + -
150D VAL* 4.6 11.9 - - + -
151D GLU 3.7 4.7 - - - -
152D ILE* 3.7 24.9 - - + +
153D GLU* 5.2 0.7 - - - -
156D LYS* 1.3 76.9 - - - +
158D LYS* 1.3 62.3 + - - +
159D VAL* 3.7 4.0 + - + +
170D ILE 3.7 0.9 - - - +
171D ALA* 3.2 4.5 - - - -
172D VAL* 2.9 43.8 + - + +
174D LEU* 4.3 7.2 - - + +
178D VAL* 6.3 2.7 - - + -
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Residues in contact with LYS 158 (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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178C VAL* 4.9 15.0 - - + +
149D LYS 3.9 1.4 - - - +
151D GLU* 2.9 66.7 + - + +
153D GLU* 4.2 20.5 - - + +
156D LYS* 6.2 3.6 - - + -
157D ALA* 1.3 70.7 - - - +
159D VAL* 1.3 60.6 + - - +
160D THR* 4.2 0.7 + - - +
169D THR* 4.2 20.2 - - + -
170D ILE 3.5 9.0 - - - +
171D ALA* 4.6 11.9 - - + -
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Residues in contact with VAL 159 (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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144D ALA* 3.2 32.8 - - + -
147D ALA* 3.4 36.6 - - + -
149D LYS 3.2 9.0 - - - +
150D VAL* 4.6 12.1 - - + -
157D ALA* 4.3 9.4 - - + +
158D LYS* 1.3 73.9 - - - +
160D THR* 1.3 64.2 + - - +
161D ARG* 3.7 6.5 + - + +
169D THR* 4.3 0.2 - - - -
170D ILE* 3.0 40.8 + - + +
172D VAL* 4.7 7.2 - - + -
178D VAL* 5.1 1.6 - - + -
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Residues in contact with THR 160 (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* 3.8 1.0 - - - -
148D SER* 2.8 32.6 + - - -
149D LYS* 3.1 36.9 + - + +
151D GLU* 4.7 7.0 - - - +
159D VAL* 1.3 72.7 - - - +
161D ARG* 1.3 61.3 + - - +
167D LEU* 4.9 15.5 - - - +
168D GLN 3.5 6.7 - - - -
169D THR* 2.9 33.2 - - + +
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Residues in contact with ARG 161 (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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69C LEU* 5.8 1.0 - - - +
93C THR 5.1 1.0 + - - -
94C ASP* 5.8 2.4 + - - +
97C ASN* 3.4 23.2 + - - +
144D ALA* 4.6 0.7 - - - +
145D THR* 2.8 51.2 + - - +
146D PHE* 3.3 24.7 - - - -
159D VAL* 3.9 15.9 - - + +
160D THR* 1.3 76.5 - - - +
162D GLU* 1.3 64.1 + - - +
163D VAL* 3.2 16.0 + - + +
167D LEU* 3.3 8.6 - - - +
168D GLN* 2.6 77.2 + - + +
170D ILE* 3.7 28.6 - - - +
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Residues in contact with GLU 162 (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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93C THR* 4.5 4.2 - - - +
237C ASN* 3.3 29.8 - - - +
238C ASP* 5.0 1.4 + - - -
146D PHE* 2.8 37.7 + - + +
148D SER* 2.7 28.0 + - - +
160D THR 4.3 0.2 + - - -
161D ARG* 1.3 68.6 - - - +
163D VAL* 1.3 60.3 + - - +
166D GLY 4.1 3.2 - - - +
167D LEU* 3.3 18.2 - - - +
181D ASP* 4.0 20.6 - - - +
183D ARG* 2.9 33.3 + - - -
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Residues in contact with VAL 163 (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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93C THR* 3.3 21.8 - - - +
94C ASP* 4.5 12.6 - - - +
238C ASP* 3.7 5.0 - - - +
246C LYS* 5.5 0.4 - - - -
146D PHE* 5.2 0.2 - - - -
161D ARG* 3.2 15.2 + - + +
162D GLU* 1.3 76.0 - - - +
164D ASP* 1.3 82.2 + - + +
165D GLY 3.3 0.5 + - - -
166D GLY 2.6 40.8 + - - +
167D LEU 3.9 1.6 - - - +
168D GLN* 3.7 39.9 - - + +
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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