Contacts of the strand formed by residues 172 - 177 (chain E) in PDB entry 5FJV
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 LYS 172 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68A GLN* 4.6 0.6 + - - -
201A GLU* 2.5 45.8 + - - -
79E MET* 4.1 3.1 - - - +
123E ASN* 3.0 38.9 + - - +
156E SER* 4.0 11.4 + - - +
170E ASN* 3.5 11.5 + - - +
171E CYS* 1.3 76.3 - - - +
173E MET* 1.3 65.6 + - - +
174E LYS* 4.7 17.9 - - + +
230E THR* 4.9 11.4 - - + +
231E TYR 3.1 10.8 - - - +
232E ALA* 5.0 1.8 - - + -
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Residues in contact with MET 173 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64E LEU* 4.8 6.1 - - - -
79E MET* 4.0 5.2 - - + -
81E THR* 3.7 17.9 - - - +
83E VAL* 4.6 9.6 - - + -
121E LEU* 4.0 9.9 - - + -
123E ASN* 3.9 4.3 - - - -
153E TYR* 3.4 42.4 - - + -
155E SER* 4.0 15.7 - - - +
172E LYS* 1.3 77.3 - - - +
174E LYS* 1.3 58.8 + - - +
175E PHE* 3.8 20.0 + - + -
229E VAL 3.8 1.6 - - - +
230E THR* 3.0 3.9 - - - -
231E TYR* 2.6 45.2 + - + +
233E PHE* 3.9 28.9 - - + -
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Residues in contact with LYS 174 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A TRP* 5.7 0.8 - - - -
199A TYR* 6.3 0.2 - - - +
201A GLU* 4.7 16.4 + - - +
121E LEU* 3.5 3.7 - - - +
122E TYR* 2.6 67.9 + - + -
123E ASN* 2.8 20.0 + - + +
172E LYS* 4.7 10.1 - - - +
173E MET* 1.3 70.8 - - - +
175E PHE* 1.3 58.6 + - - +
217E LYS* 4.5 7.7 - - - +
219E TYR* 2.9 35.9 + - - -
228E ASP* 3.8 23.6 - - + +
230E THR* 3.4 26.0 - - + +
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Residues in contact with PHE 175 (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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62E PHE* 3.7 25.3 - + + -
64E LEU* 4.5 11.0 - - + -
85E LEU* 3.9 23.1 - - + -
119E ILE* 4.2 10.1 - - + -
120E VAL 3.4 16.6 - - - -
121E LEU* 4.0 19.3 - - + -
122E TYR* 3.7 3.8 - - - -
153E TYR* 4.0 23.3 - + - -
173E MET* 4.1 37.2 - - + -
174E LYS* 1.3 74.2 - - - +
176E GLY* 1.3 56.9 + - - +
187E LEU* 5.2 0.2 - - - +
228E ASP* 3.1 5.0 - - - +
229E VAL 2.6 44.7 + - - +
231E TYR* 4.1 24.2 - + - -
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Residues in contact with GLY 176 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119E ILE* 4.0 9.8 - - - +
120E VAL* 3.1 20.9 + - - +
122E TYR* 3.2 21.5 - - - -
175E PHE* 1.3 77.2 - - - +
177E SER* 1.3 66.6 + - - -
178E TRP 3.5 0.5 + - - -
187E LEU* 4.5 7.9 - - - -
227E PRO 3.9 12.3 - - - -
228E ASP* 4.3 0.9 - - - -
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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
----------------------------------------------------------
118E ASP* 3.1 22.2 - - - -
119E ILE* 4.1 12.7 - - - +
122E TYR* 3.2 14.2 + - - -
176E GLY* 1.3 69.6 - - - -
178E TRP* 1.3 61.9 + - - +
180E TYR* 2.9 30.6 + - - -
185E ILE* 4.4 22.7 + - - +
187E LEU* 4.6 9.7 - - - +
226E TYR* 4.2 8.0 - - - +
227E PRO* 4.5 8.0 + - - +
300E EPJ 4.2 4.0 + - - -
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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