Contacts of the strand formed by residues 60 - 66 (chain E) in PDB entry 5OF4
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 60 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58E MET* 3.9 12.1 - - + +
59E ARG* 1.3 75.5 + - - +
61E LEU* 1.3 62.0 + - - +
62E TYR* 3.7 7.6 + - - -
101E ILE 5.7 1.4 + - - -
102E SER* 5.8 0.4 - - - -
103E GLN* 3.0 45.7 + - + -
120E LEU* 4.2 10.3 - - + -
156E LEU* 4.0 24.4 - - + +
159E MET* 4.1 18.3 - - + +
160E PRO* 5.2 1.8 - - + -
163E THR* 3.1 34.6 + - + -
164E SER 3.6 15.6 + - - +
165E ARG* 4.4 8.2 - - - +
166E GLU 2.8 18.8 + - - +
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Residues in contact with LEU 61 (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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59E ARG* 3.5 30.1 - - + +
60E HIS* 1.3 75.6 - - - +
62E TYR* 1.3 63.8 + - - +
63E VAL* 4.8 4.0 - - + -
91E PHE* 4.1 21.5 - - + -
95E TYR* 3.2 37.9 - - + +
103E GLN 2.8 6.9 + - - +
104E ILE* 2.9 35.7 - - + +
105E GLY 2.9 3.1 + - - -
120E LEU* 4.7 0.2 - - - -
166E GLU* 3.5 38.8 - - + +
167E VAL* 4.5 1.3 - - - +
168E LEU* 5.0 9.2 - - + +
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Residues in contact with TYR 62 (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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60E HIS 3.7 6.3 + - - -
61E LEU* 1.3 74.8 - - - +
63E VAL* 1.3 64.7 + - - +
64E VAL* 3.3 0.7 + - + +
105E GLY* 3.1 22.9 - - - +
107E ILE* 3.5 34.3 - - + -
116E LYS* 4.6 14.4 - - + -
118E THR 4.7 1.6 - - - -
120E LEU* 3.2 53.1 + - + +
151E ILE* 5.8 0.4 - - + -
152E ALA* 4.9 9.0 - - + -
155E THR* 3.3 30.0 + - - +
156E LEU* 4.5 26.0 - - + -
166E GLU 4.1 4.4 + - - -
167E VAL* 3.3 26.4 - - + +
168E LEU 3.2 13.1 + - - +
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Residues in contact with VAL 63 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61E LEU* 3.8 4.4 - - + -
62E TYR* 1.3 71.7 - - - +
64E VAL* 1.3 60.4 + - - +
65E VAL* 3.7 15.5 + - + +
88E LEU* 3.7 25.1 - - + -
91E PHE* 4.3 21.8 - - + -
104E ILE* 4.1 20.9 - - + -
105E GLY 2.9 9.4 + - - +
106E ILE* 3.6 5.9 - - + -
107E ILE 2.9 27.0 + - - +
168E LEU* 3.3 18.4 - - + +
170E ILE* 3.8 17.7 - - + -
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Residues in contact with VAL 64 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62E TYR* 3.6 14.4 - - + +
63E VAL* 1.3 71.1 - - - +
65E VAL* 1.3 61.7 + - - +
107E ILE* 3.2 17.5 - - + +
109E THR* 3.5 11.9 - - - +
145E LEU* 5.6 1.6 - - + -
148E SER* 3.4 39.0 - - - +
149E LEU* 6.0 0.4 - - + -
167E VAL* 3.8 15.7 - - + -
168E LEU 2.7 14.3 + - - +
169E ILE* 3.9 22.2 - - + -
170E ILE* 2.7 34.6 + - - +
171E PHE* 5.9 4.0 - - + -
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Residues in contact with VAL 65 (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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63E VAL* 3.8 14.1 - - + +
64E VAL* 1.3 79.4 - - - +
66E ASP* 1.3 72.2 + - - +
71E MET* 6.0 0.7 - - - -
81E LEU* 4.2 17.5 - - + -
84E THR* 4.1 24.5 - - + -
88E LEU* 3.6 25.8 - - + -
106E ILE* 4.8 13.0 - - + -
107E ILE 2.9 8.0 + - - +
108E VAL* 3.6 11.6 - - + -
109E THR* 2.8 30.1 + - - -
131E LEU* 6.4 0.7 - - + -
170E ILE* 3.5 5.6 - - + -
171E PHE* 6.3 0.2 - - - -
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Residues in contact with ASP 66 (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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65E VAL* 1.3 87.2 - - - +
67E GLY* 1.3 76.3 + - - +
68E SER* 3.1 11.1 + - - -
71E MET* 3.8 18.2 - - + +
81E LEU* 4.7 4.5 - - - +
108E VAL* 5.2 2.7 - - - +
109E THR* 3.8 4.5 - - - +
139E CYS* 5.0 0.2 - - - -
143E PRO* 3.2 23.7 - - - +
170E ILE* 3.2 9.8 + - - +
171E PHE* 3.3 20.9 - - + -
172E SER* 2.5 52.3 + - - +
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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