Contacts of the strand formed by residues 177 - 186 (chain E) in PDB entry 4S0H
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 HIS 177 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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110E ASP 5.6 2.0 - - - +
112E HIS 3.9 9.6 + - - +
113E ARG* 4.1 23.5 - - + +
114E TYR* 4.8 0.4 - - - -
127E ALA* 3.3 30.5 - - + -
128E GLU* 2.8 44.2 + - + +
174E ASN* 3.2 22.0 + - + +
175E SER 3.0 17.6 + - - -
176E MET* 1.3 82.0 - - - +
178E LYS* 1.3 62.9 + - - +
179E TYR* 3.5 18.6 - - + +
212E ILE* 3.4 4.7 - - - -
213E ALA 3.0 24.6 + - - -
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Residues in contact with LYS 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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68E HIS* 5.7 5.1 - - - -
108E PRO* 3.7 3.8 - - - +
109E ALA* 2.8 37.8 + - + +
110E ASP* 3.9 20.7 + - - +
112E HIS 4.6 1.6 + - - -
114E TYR* 3.8 33.6 - - + +
177E HIS* 1.3 77.1 - - - +
179E TYR* 1.3 67.2 + - - +
210E ALA* 4.2 20.0 - - - +
211E PHE 3.3 12.4 - - - +
212E ILE* 4.1 17.0 - - + +
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Residues in contact with TYR 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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106E ILE* 3.6 29.4 - - + -
107E VAL 3.6 12.6 - - - -
108E PRO* 4.1 15.5 - - + -
109E ALA* 4.2 3.9 - - - +
173E LEU* 3.5 19.6 - - + -
174E ASN* 2.4 58.3 + - - +
177E HIS* 3.5 26.4 - - + +
178E LYS* 1.3 77.0 - - - +
180E GLN* 1.3 61.2 + - - +
181E PRO* 4.3 1.3 - - - -
210E ALA* 3.2 7.1 - - - +
211E PHE* 2.5 47.2 + + + +
213E ALA* 3.6 20.0 - - + -
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Residues in contact with GLN 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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106E ILE* 4.4 1.1 - - - -
107E VAL* 2.7 45.7 + - + +
108E PRO 5.0 0.2 - - - -
109E ALA* 4.6 11.8 - - + +
179E TYR* 1.3 75.2 - - - +
181E PRO* 1.4 96.1 + - - +
182E ARG* 3.7 4.6 + - + -
205E VAL* 3.5 25.3 - - + +
206E PHE 3.1 22.6 + - - -
207E PRO* 3.8 12.1 - - - +
209E THR* 3.6 0.8 + - - -
210E ALA* 3.4 19.8 - - + +
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Residues in contact with PRO 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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64E TRP* 5.9 0.2 - - + -
83E MET* 4.8 7.0 - - - -
87E TYR* 4.3 18.7 + - + -
104E MET* 4.5 7.4 - - + -
105E ASP 3.6 6.5 - - - +
106E ILE* 3.8 16.8 - - + -
180E GLN* 1.4 110.5 + - - +
182E ARG* 1.3 61.5 + - - +
204E HIS 4.5 0.2 - - - +
205E VAL* 4.3 6.8 - - - +
206E PHE 4.8 0.2 + - - -
209E THR* 3.1 40.4 + - - +
211E PHE* 3.5 20.4 - - + -
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Residues in contact with ARG 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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101A ILE* 3.8 12.7 - - - +
186A VAL* 4.1 5.3 - - - +
187A LYS* 2.8 30.1 + - - +
188A ALA* 4.4 3.7 + - - +
87E TYR* 4.7 0.9 - - - -
104E MET* 3.0 22.0 - - - +
105E ASP* 2.7 53.2 + - - +
107E VAL* 3.3 33.7 - - + +
180E GLN* 3.8 11.9 - - + +
181E PRO* 1.3 80.6 - - - +
183E LEU* 1.3 60.7 + - - +
184E HIS* 3.6 28.9 + - + +
203E THR* 4.1 8.7 - - + +
204E HIS 3.7 4.3 - - - +
205E VAL* 3.8 25.1 - - + -
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Residues in contact with LEU 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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56E VAL* 3.9 38.8 - - + -
87E TYR* 4.0 18.2 + - + +
89E VAL* 4.3 13.0 - - + -
91E VAL* 5.0 1.1 - - + -
102E LEU* 4.1 14.6 - - + -
103E LEU 3.3 19.1 - - - +
104E MET* 4.2 1.6 - - + -
155E PHE* 3.4 29.4 - - + -
182E ARG* 1.3 73.0 - - - +
184E HIS* 1.3 68.1 + - - +
185E ILE* 4.3 12.6 - - + -
202E CYS 4.1 0.3 - - - -
203E THR* 3.1 6.4 - - - -
204E HIS* 2.8 40.1 + - + +
206E PHE* 6.1 0.2 - - + -
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Residues in contact with HIS 184 (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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186A VAL* 4.2 9.8 - - + +
201A PHE* 3.7 15.8 - + + -
101E ILE 3.7 1.0 - - - +
102E LEU* 3.6 4.5 - - - -
103E LEU* 3.0 61.8 + - + +
105E ASP* 2.6 35.7 + - - -
135E LEU* 5.4 0.4 - - + -
182E ARG* 3.6 32.7 - - - +
183E LEU* 1.3 77.0 - - - +
185E ILE* 1.3 63.1 + - - +
186E VAL* 3.9 0.7 - - + -
202E CYS 3.0 5.8 + - - +
203E THR* 2.8 33.7 + - + -
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Residues in contact with ILE 185 (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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54E ILE* 4.6 22.7 - - + -
56E VAL* 4.5 13.9 - - + -
91E VAL* 4.7 14.1 - - + -
94E LEU* 4.6 6.7 - - + -
100E TYR* 3.5 32.3 - - + -
101E ILE 3.5 2.9 - - - -
102E LEU* 3.9 27.6 - - + -
183E LEU* 4.3 19.5 - - + -
184E HIS* 1.3 74.8 - - - +
186E VAL* 1.3 62.2 + - - +
200E ALA 3.5 18.7 - - - +
202E CYS* 3.0 23.4 + - + -
204E HIS* 4.6 9.0 - - + -
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Residues in contact with VAL 186 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105A ASP* 4.2 5.6 - - - +
135A LEU* 5.1 9.4 - - + -
182A ARG* 3.2 24.7 - - - +
184A HIS* 4.0 9.2 - - + +
201A PHE* 4.0 19.3 - - + -
100E TYR* 3.2 14.1 - - - -
101E ILE* 2.9 38.2 + - + +
103E LEU* 3.8 28.7 - - + -
184E HIS* 5.0 0.7 - - + -
185E ILE* 1.3 75.3 - - - +
187E LYS* 1.3 75.8 + - - +
200E ALA* 4.6 0.2 - - - -
201E PHE* 3.3 15.0 - - + -
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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