Contacts of the strand formed by residues 178 - 184 (chain A) in PDB entry 5EN4
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 ARG 178 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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133A GLN 5.8 2.2 + - - -
134A GLY 3.4 7.5 + - - -
135A ASN* 3.1 26.4 - - + +
136A VAL 2.9 24.7 + - - -
176A GLY 4.4 8.8 + - - +
177A VAL* 1.3 75.0 - - - +
179A VAL* 1.3 65.0 + - - +
180A ASN* 3.7 10.6 - - - +
231A LEU 2.8 21.6 + - - -
232A ALA 3.1 26.5 + - - -
235A ALA* 2.9 21.1 + - - +
236A ASN* 3.5 37.1 + - - +
237A PHE 5.3 0.2 - - - -
238A CYS 3.3 25.2 + - - +
239A THR* 3.5 11.7 - - - +
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Residues in contact with VAL 179 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122A THR* 6.1 0.4 - - + -
126A LEU* 5.8 0.4 - - + -
136A VAL* 3.4 34.1 - - + -
138A ASN* 4.3 5.4 - - - +
165A THR* 3.6 26.0 - - + +
168A LEU* 4.0 24.7 - - + +
169A ALA* 3.8 21.6 - - - +
172A GLU* 4.5 4.7 - - + -
177A VAL* 4.4 12.1 - - + +
178A ARG* 1.3 79.2 - - - +
180A ASN* 1.3 58.2 + - - +
239A THR* 3.1 6.1 + - - -
240A GLY* 2.7 33.8 + - - -
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Residues in contact with ASN 180 (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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135A ASN* 5.7 1.8 + - - +
136A VAL 3.0 9.1 + - - +
137A ILE* 3.3 8.1 - - + +
138A ASN* 2.9 23.6 + - - +
165A THR* 3.5 9.0 - - - +
178A ARG* 3.7 20.4 - - - +
179A VAL* 1.3 76.1 - - - +
181A CYS* 1.3 61.9 + - - +
231A LEU* 4.1 29.7 + - + +
238A CYS 3.1 20.7 + - - -
239A THR* 3.2 6.7 + - - +
240A GLY 3.1 7.6 + - - -
241A ILE* 3.1 36.6 + - + +
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Residues in contact with CYS 181 (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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137A ILE* 5.0 0.2 - - - -
138A ASN* 3.1 17.5 - - + +
140A SER* 4.6 4.9 - - - -
162A THR* 4.1 24.0 - - - -
165A THR* 3.7 20.6 - - - +
166A LYS* 6.4 0.2 - - - -
180A ASN* 1.3 76.7 - - - +
182A ILE* 1.3 64.5 + - - +
183A SER* 4.5 3.4 - - - -
231A LEU* 4.5 2.6 - - - +
241A ILE 2.9 20.8 + - - +
242A GLU* 3.4 23.5 - - - -
243A LEU* 2.9 26.7 + - - +
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Residues in contact with ILE 182 (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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137A ILE* 3.9 15.5 - - + -
138A ASN 2.9 5.7 + - - -
139A ILE* 3.5 16.1 - - + -
140A SER 2.8 25.1 + - - -
181A CYS* 1.3 72.7 - - - +
183A SER* 1.3 62.9 + - - +
184A PRO* 3.3 13.3 - - + +
224A VAL* 4.1 19.1 - - + +
227A ALA* 4.1 7.0 - - + -
228A ALA* 3.7 38.4 - - + +
231A LEU* 3.6 20.4 - - + -
243A LEU* 3.4 14.8 - - + +
245A VAL* 3.8 20.6 - - + -
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Residues in contact with SER 183 (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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140A SER* 3.6 10.2 - - - -
141A SER 3.6 26.2 + - - +
142A LEU 3.7 1.3 + - - -
181A CYS* 4.1 0.5 - - - -
182A ILE* 1.3 72.1 - - - +
184A PRO* 1.3 66.6 - - - +
242A GLU* 2.7 34.3 + - - +
243A LEU 2.9 8.5 + - - +
244A LEU* 3.6 16.0 - - - -
245A VAL 3.1 19.2 + - - -
246A THR* 3.6 5.7 - - - +
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Residues in contact with PRO 184 (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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21A ILE* 4.5 8.3 - - + -
139A ILE* 4.0 16.8 - - + -
140A SER 3.6 16.4 - - - +
141A SER* 3.8 0.7 + - - -
142A LEU* 2.9 21.6 + - - +
182A ILE* 3.3 20.2 - - + +
183A SER* 1.3 84.9 - - - +
185A GLY* 1.3 59.3 + - - +
187A ILE* 3.7 24.9 - - + -
224A VAL* 4.5 9.6 - - + -
245A VAL* 3.2 11.4 - - + +
246A THR* 4.2 0.7 - - - -
301A NAD 3.3 22.1 - - + -
302A 5Q6 4.6 0.2 - - - -
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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