Contacts of the strand formed by residues 168 - 174 (chain E) in PDB entry 4P5K
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 168 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130E PHE 3.8 0.3 - - - +
131E LEU* 3.4 4.3 - - - +
132E ASN* 2.8 42.3 + - - +
133E GLY 4.6 0.7 + - - -
166E GLY 5.6 1.6 - - - +
167E ASP* 1.3 74.7 - - - +
169E TYR* 1.3 71.0 - - - +
170E THR* 4.0 9.7 + - - +
185E GLU* 3.2 31.4 - - + +
186E TRP 3.7 4.0 - - - +
187E LYS* 4.4 18.6 - - + +
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Residues in contact with TYR 169 (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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113E LEU* 3.7 29.6 - - + -
129E TRP* 4.2 4.9 - - + -
130E PHE 3.2 7.9 - - - +
131E LEU* 3.9 32.1 - - + +
136E GLU* 6.3 0.7 - - + -
159E LEU* 3.9 18.6 - - + -
161E MET* 3.5 31.8 - - + +
162E THR 3.7 4.9 + - - -
163E PRO* 3.4 36.5 - - + +
167E ASP* 4.2 16.2 + - + -
168E VAL* 1.3 74.3 - - - +
170E THR* 1.3 61.4 + - - +
184E VAL 4.4 0.2 - - - +
185E GLU* 3.2 5.9 - - - +
186E TRP* 2.8 51.8 + + + +
188E ALA* 4.7 4.9 - - + -
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Residues in contact with THR 170 (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 ARG 3.9 0.5 - - - +
129E TRP* 3.2 9.2 - - - -
130E PHE* 2.8 56.2 + - + +
133E GLY* 5.5 2.9 + - - -
168E VAL* 4.1 12.6 + - - +
169E TYR* 1.3 76.6 + - - +
171E CYS* 1.3 66.0 + - - +
172E GLN* 3.9 1.5 + - + +
183E THR* 3.7 35.2 - - + -
184E VAL 3.8 11.4 - - - +
185E GLU* 4.4 6.1 - - + +
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Residues in contact with CYS 171 (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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97E VAL* 4.4 4.0 - - + -
99E VAL* 3.8 10.8 - - + -
115E CYS* 2.0 53.2 - - + -
127E VAL* 3.9 16.8 - - - -
128E ARG 3.8 3.6 - - - -
129E TRP* 3.7 12.9 - - + -
170E THR* 1.3 72.9 - - - +
172E GLN* 1.3 63.8 + - - +
173E VAL* 4.5 3.7 - - - +
182E VAL 3.8 1.2 - - - +
183E THR* 3.5 4.2 - - - -
184E VAL* 2.9 38.9 + - - +
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Residues in contact with GLN 172 (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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126E GLN 3.6 1.0 - - - +
127E VAL* 3.3 4.1 - - - -
128E ARG* 2.8 46.4 + - - +
130E PHE* 3.8 34.3 - - + -
170E THR* 3.9 1.5 + - + +
171E CYS* 1.3 76.0 - - - +
173E VAL* 1.3 67.8 + - - +
174E GLU* 2.9 30.7 + - - +
181E PRO* 4.4 13.6 - - + +
182E VAL 3.6 4.3 - - - +
183E THR* 4.1 24.2 - - + +
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Residues in contact with VAL 173 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95E PRO* 4.0 26.7 - - + -
97E VAL* 3.9 30.3 - - + -
117E VAL* 4.1 20.2 - - + -
125E ILE* 4.2 13.7 - - + -
126E GLN 3.3 6.7 - - - +
127E VAL* 4.4 9.2 - - + -
171E CYS* 4.5 5.2 - - - -
172E GLN* 1.3 77.5 - - - +
174E GLU* 1.3 61.8 + - - +
178E LEU* 4.1 9.4 - - + +
181E PRO* 3.6 5.4 - - - +
182E VAL* 3.1 35.8 + - + +
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Residues in contact with GLU 174 (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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125E ILE* 3.6 3.8 - - - +
126E GLN* 2.8 76.1 + - - +
128E ARG* 3.5 29.5 + - - +
172E GLN* 2.9 40.8 + - - +
173E VAL* 1.3 75.9 - - - +
175E HIS* 1.3 62.8 + - - +
178E LEU* 4.7 0.4 - - - -
181E PRO* 4.5 19.1 - - + -
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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