Contacts of the strand formed by residues 176 - 183 (chain E) in PDB entry 6S1M
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 GLY 176 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154E ILE* 3.8 4.3 - - - +
172E SER* 3.5 0.6 - - - -
173E GLY 2.7 35.8 + - - +
174E GLU 3.0 8.9 + - - -
175E LEU* 1.3 78.4 - - - +
177E ASN* 1.3 61.5 + - - +
115G GLU 3.5 10.5 - - - -
117G LYS* 3.9 23.0 - - - +
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Residues in contact with ASN 177 (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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154E ILE* 3.5 8.5 - - - -
171E ALA 2.8 21.1 - - - +
172E SER* 3.2 17.7 - - - -
175E LEU 3.9 0.6 + - - -
176E GLY* 1.3 76.8 - - - -
178E GLY* 1.3 59.0 + - - +
179E ASN* 4.9 5.7 + - - -
78G ILE* 6.1 0.2 - - - +
114G TYR* 3.7 3.7 - - - +
115G GLU* 2.8 47.7 + - - +
117G LYS* 6.3 0.8 - - - +
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Residues in contact with GLY 178 (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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151E LEU* 4.1 7.4 - - - +
154E ILE* 3.8 4.6 - - - +
170E SER* 3.4 1.7 - - - -
171E ALA 3.0 30.4 + - - +
177E ASN* 1.3 77.6 - - - +
179E ASN* 1.3 67.0 + - - +
113G ASP 3.0 14.1 - - - -
114G TYR* 3.8 14.8 - - - -
115G GLU* 5.6 0.4 - - - -
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Residues in contact with ASN 179 (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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151E LEU* 4.6 1.5 - - - +
168E LYS* 4.3 21.7 - - + +
169E PHE 3.0 16.8 - - - +
170E SER* 3.2 17.6 - - - +
177E ASN* 4.9 6.1 + - - -
178E GLY* 1.3 77.9 + - - -
180E ILE* 1.3 63.6 + - - +
181E LYS* 4.5 11.5 - - - +
111G VAL 3.8 1.2 - - - +
112G SER* 3.5 1.1 - - - -
113G ASP* 2.8 53.9 + - - +
114G TYR* 4.8 2.0 - - - -
115G GLU* 6.0 1.0 - - - +
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Residues in contact with ILE 180 (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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147E ILE* 3.5 55.9 - - + +
150E ASP* 4.3 7.9 - - + +
151E LEU* 4.2 9.2 - - + -
167E VAL 4.0 0.3 - - - +
168E LYS* 3.5 5.0 - - - +
169E PHE* 2.8 34.6 + - + +
179E ASN* 1.3 80.1 - - - +
181E LYS* 1.3 66.5 + - - +
182E LEU* 5.0 1.3 - - + -
110G LYS* 3.7 35.4 - - + -
111G VAL 3.4 3.6 - - - +
112G SER* 3.8 15.7 - - - +
114G TYR* 4.1 19.1 - - - +
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Residues in contact with LYS 181 (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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167E VAL 3.7 5.2 - - - +
168E LYS* 3.9 32.3 - - + +
179E ASN* 4.5 11.9 - - - +
180E ILE* 1.3 78.9 - - - +
182E LEU* 1.3 63.6 + - - +
183E SER* 4.3 4.2 + - - +
109G GLU 3.6 0.9 - - - +
110G LYS* 3.3 8.0 - - - -
111G VAL* 2.9 42.8 + - + +
113G ASP* 6.5 0.2 - - - -
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Residues in contact with LEU 182 (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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139E MET* 3.5 37.0 - - + -
143E GLU* 4.0 21.3 - - + +
147E ILE* 4.0 18.6 - - + -
166E GLY* 3.2 3.1 - - - -
167E VAL* 2.9 50.0 + - + +
169E PHE* 4.3 3.6 - - + -
180E ILE* 4.2 2.2 + - + -
181E LYS* 1.3 73.5 - - - +
183E SER* 1.3 64.8 + - - +
195E VAL* 4.4 17.7 - - + -
197E ILE* 5.0 0.4 - - - -
109G GLU* 3.5 4.9 - - + +
110G LYS* 3.7 35.4 - - + -
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Residues in contact with SER 183 (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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165E ASP* 4.7 10.8 + - - +
166E GLY* 4.2 8.6 - - - -
181E LYS* 5.1 5.0 + - - +
182E LEU* 1.3 77.5 + - - +
184E GLN* 1.3 71.0 + - - +
185E THR* 3.6 6.1 + - - +
195E VAL* 4.0 15.0 - - - +
197E ILE* 4.7 0.2 - - - -
108G GLN 6.0 0.2 - - - -
109G GLU* 3.4 20.9 + - - +
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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