Contacts of the strand formed by residues 156 - 162 (chain E) in PDB entry 4NQD
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 VAL 156 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10E PHE* 4.5 7.1 - - - -
124E PRO* 4.6 1.6 - - + -
151E PHE* 3.5 52.0 - - + -
154E ASP* 3.7 11.7 + - - +
155E HIS* 1.3 79.7 - - - +
157E GLU* 1.3 69.1 + - - +
158E LEU 4.2 0.2 - - - -
191E LEU* 4.1 18.6 - - + +
213E VAL* 3.9 23.1 - - + -
214E GLN 3.3 5.4 - - - +
215E PHE* 4.1 11.9 - - + -
216E TYR* 5.0 0.4 - - - -
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Residues in contact with GLU 157 (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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9E LYS* 5.4 2.3 - - - +
10E PHE* 3.5 19.3 - - + -
156E VAL* 1.3 79.3 - - - +
158E LEU* 1.3 59.3 + - - +
159E SER* 4.2 1.3 + - - -
212E GLN 3.6 2.1 - - - +
213E VAL* 3.4 3.1 - - - -
214E GLN* 2.8 45.1 + - + +
216E TYR* 2.6 36.6 + - + -
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Residues in contact with LEU 158 (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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146E CYS* 4.1 7.2 - - + +
148E ALA* 4.5 6.3 - - + -
156E VAL 4.2 0.4 - - - -
157E GLU* 1.3 71.8 - - - +
159E SER* 1.3 67.1 + - - +
160E TRP* 4.0 9.4 - - + +
173E THR* 4.0 13.9 + - + +
191E LEU* 4.2 35.1 - - + +
193E SER* 3.5 36.8 - - - +
211E CYS* 3.9 21.5 - - - -
212E GLN 3.3 4.0 - - - -
213E VAL* 3.8 25.8 - - + +
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Residues in contact with SER 159 (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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157E GLU 5.1 1.3 + - - -
158E LEU* 1.3 77.9 - - - +
160E TRP* 1.3 65.1 + - - +
161E TRP* 3.1 18.5 + - - -
166E GLU* 3.4 30.5 - - - -
211E CYS* 3.6 2.8 - - - -
212E GLN* 2.9 42.1 + - - +
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Residues in contact with TRP 160 (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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128E VAL* 4.4 7.2 - - + -
144E LEU* 3.8 37.9 - - + -
145E VAL 4.1 2.7 - - - -
146E CYS* 3.5 32.1 - - + -
158E LEU* 4.0 4.8 - - + +
159E SER* 1.3 75.7 - - - +
161E TRP* 1.3 60.9 + - - +
166E GLU* 3.3 9.5 - - - +
167E VAL* 3.0 47.1 + - + +
171E VAL* 3.6 27.6 - - + -
193E SER* 2.9 40.4 + - - -
194E ARG 3.9 3.2 + - - -
195E LEU* 3.7 31.4 - - + -
209E PHE* 4.8 2.7 - - + -
210E ARG 3.3 23.3 - - - -
211E CYS* 4.2 12.3 - - + -
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Residues in contact with TRP 161 (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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159E SER* 3.1 30.6 + - - -
160E TRP* 1.3 77.3 - - - +
162E VAL* 1.3 62.4 + - - +
163E ASN 4.2 0.2 - - - -
164E GLY* 3.5 25.1 - - - -
165E LYS* 3.3 6.3 - - - +
166E GLU* 3.4 43.5 - - + -
208E HIS* 3.8 2.1 - - - +
209E PHE* 3.4 4.2 - - - -
210E ARG* 2.8 80.9 + - - +
212E GLN* 3.8 23.1 + - + -
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Residues in contact with VAL 162 (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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160E TRP 4.2 0.2 - - - -
161E TRP* 1.3 76.6 - - - +
163E ASN* 1.3 70.4 + - + +
164E GLY 3.2 1.3 - - - -
165E LYS* 2.7 34.2 + - - +
167E VAL* 3.8 27.7 - - + +
195E LEU* 3.7 30.5 - - + -
201E PHE* 3.5 36.1 - - + -
208E HIS 3.5 6.3 - - - +
209E PHE* 3.8 10.8 - - + -
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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