Contacts of the strand formed by residues 174 - 183 (chain E) in PDB entry 6PI7
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 TYR 174 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13E SER* 5.4 0.2 + - - -
104E LYS* 4.5 5.6 - - - -
106E GLU* 3.2 32.5 + - - +
139E ASN* 3.1 6.8 + - - -
140E PHE* 2.8 55.8 + - + -
141E TYR* 3.8 21.8 - + - -
143E ARG* 3.7 57.4 - - + -
164E VAL* 4.4 4.9 - - + -
165E THR* 3.6 22.0 - - - -
167E GLN* 3.3 39.0 + - + +
173E THR* 1.3 73.6 - - - +
175E SER* 1.3 61.5 + - - +
178F HIS* 5.9 1.1 - - - -
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Residues in contact with SER 175 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136E LEU* 6.2 0.4 - - - -
137E LEU 3.2 9.9 - - - -
138E ASN* 3.5 3.4 - - - -
139E ASN* 2.9 24.3 + - - -
140E PHE* 3.6 3.4 - - - -
164E VAL* 3.4 4.6 - - - +
165E THR* 3.0 37.6 + - - -
174E TYR* 1.3 69.3 + - - +
176E LEU* 1.3 60.0 + - - +
178F HIS* 3.3 36.3 + - - -
180F PHE* 3.6 13.6 - - - -
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Residues in contact with LEU 176 (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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136E LEU* 3.7 2.3 - - - -
137E LEU* 2.8 43.9 + - + +
140E PHE* 3.4 20.6 - - + -
143E ARG* 5.5 3.6 - - + +
145E ALA* 5.4 10.8 - - + +
147E VAL* 4.0 18.4 - - + -
162E GLU* 3.5 29.4 - - + +
163E SER 3.3 10.8 - - - +
164E VAL* 3.6 23.1 - - + -
175E SER* 1.3 74.0 - - - +
177E SER* 1.3 75.3 + - - +
178E SER 4.0 2.2 - - - +
180F PHE* 3.8 6.9 - - - -
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Residues in contact with SER 177 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134E VAL* 4.8 12.1 - - - -
135E CYS 3.3 7.2 - - - -
136E LEU* 4.7 1.8 - - - +
161E GLN 4.0 0.7 + - - +
162E GLU* 3.3 5.0 - - - -
163E SER* 3.0 38.0 + - - +
176E LEU* 1.3 78.4 - - - +
178E SER* 1.3 58.6 + - - +
179E THR* 4.3 5.3 + - - -
180F PHE* 3.6 36.4 - - - +
193F SER* 4.8 6.5 + - - -
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Residues in contact with SER 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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134E VAL* 3.4 3.1 - - - +
135E CYS* 2.8 38.3 + - - -
147E VAL* 3.9 15.2 - - - +
149E TRP* 3.1 27.7 + - - -
160E SER* 4.3 3.8 - - - -
161E GLN 3.5 5.6 + - - -
162E GLU* 2.9 29.2 + - - +
176E LEU* 4.0 3.6 - - - +
177E SER* 1.3 72.3 - - - +
179E THR* 1.3 62.3 + - - +
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Residues in contact with THR 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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132E SER* 4.1 21.3 - - - +
133E VAL 3.3 9.2 - - - +
134E VAL* 3.8 16.8 - - + +
160E SER* 3.1 8.0 - - - -
161E GLN* 3.0 36.7 + - - +
177E SER* 4.9 5.4 + - - -
178E SER* 1.3 75.4 + - - +
180E LEU* 1.3 60.0 + - - +
181E THR* 3.9 17.3 + - - +
155F LEU* 5.2 8.6 - - + +
183F VAL* 6.5 0.9 - - - -
193F SER* 5.2 3.1 + - - -
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Residues in contact with LEU 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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131E ALA 3.7 1.6 - - - +
132E SER* 3.4 3.6 - - - -
133E VAL* 2.9 38.8 + - + +
149E TRP* 3.6 59.6 - - + -
151E VAL* 3.9 25.4 - - + -
156E GLN* 4.0 2.9 - - + -
159E ASN* 3.2 43.7 - - - +
160E SER* 4.3 1.1 - - - -
179E THR* 1.3 70.5 - - - +
181E THR* 1.3 58.7 + - - +
182E LEU* 4.1 17.7 - - + -
193E TYR* 4.4 6.7 - - + -
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Residues in contact with THR 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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130E THR* 4.1 22.0 - - + -
131E ALA 3.5 3.1 - - - +
132E SER* 4.4 6.8 + - - +
159E ASN* 3.0 24.1 + - - +
160E SER* 5.4 0.2 - - - -
161E GLN* 5.4 4.5 + - - +
179E THR* 3.9 19.8 + - - +
180E LEU* 1.3 73.0 - - - +
182E LEU* 1.3 69.4 + - - +
157F LYS* 4.9 8.5 - - - -
185F GLN* 5.6 2.8 + - - +
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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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130E THR* 3.5 7.9 - - - +
131E ALA 2.9 36.2 + - - +
133E VAL* 4.9 3.6 - - + -
151E VAL* 4.8 3.6 - - + -
156E GLN* 4.5 4.7 - - - +
159E ASN* 3.5 28.5 - - + +
180E LEU* 4.1 18.8 - - + +
181E THR* 1.3 78.8 - - - +
183E SER* 1.3 66.2 + - - +
186E ASP* 4.5 12.6 - - + +
187E TYR* 4.3 17.9 - - + +
190E HIS* 6.0 0.9 - - - +
193E TYR* 3.6 36.3 - - + +
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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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129E GLY 4.1 7.0 - - - -
130E THR* 4.7 2.7 - - - +
131E ALA 4.6 0.4 - - - -
182E LEU* 1.3 75.8 - - - +
184E LYS* 1.3 57.6 + - - +
185E ALA* 3.7 7.7 + - - +
186E ASP* 3.1 33.1 + - - +
187E TYR* 2.9 27.5 + - - +
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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