Contacts of the strand formed by residues 143 - 147 (chain C) in PDB entry 1EFP
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 143 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85C SER 3.0 11.9 + - - +
86C HIS* 3.5 22.9 - - + +
87C ILE 3.0 16.5 + - - -
111C LEU* 5.1 3.1 - - + -
120C ALA 3.8 8.5 + - - +
121C ASP* 3.4 34.9 + - - +
123C PHE* 3.8 21.8 - - + -
138C SER* 3.7 26.5 + - - +
139C LYS 5.0 0.2 - - - -
140C ASP 2.9 24.4 + - - +
141C ALA 4.7 4.3 + - - +
142C LYS* 1.3 76.9 - - - +
144C VAL* 1.3 62.4 + - - +
145C PHE* 3.0 23.3 - - + -
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Residues in contact with VAL 144 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87C ILE* 3.3 16.8 - - + +
99C MET* 3.4 45.5 - - + +
102C VAL* 4.5 5.4 - - + -
103C ALA* 4.0 18.4 - - + +
106C LEU* 4.4 13.7 - - + -
108C VAL* 3.8 25.5 - - + +
109C MET 4.1 5.0 + - - +
110C VAL* 3.6 9.4 - - + -
111C LEU* 3.2 20.5 + - - +
142C LYS* 3.5 6.7 + - + +
143C LYS* 1.3 74.2 - - - +
145C PHE* 1.3 65.7 + - - +
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Residues in contact with PHE 145 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26C VAL* 4.6 4.3 - - + -
29C LEU* 4.5 8.7 - - + -
86C HIS* 3.7 27.6 - + + -
87C ILE 3.1 7.0 + - - -
88C ALA* 3.2 36.7 - - + -
89C ALA 3.4 2.3 + - - -
99C MET* 3.5 8.0 - - - +
110C VAL* 4.4 2.7 - - - -
111C LEU* 3.0 29.6 - - + +
114C VAL* 4.1 12.1 - - + -
117C ILE* 4.0 11.0 - - + -
123C PHE* 3.9 17.3 - + - -
143C LYS* 3.0 30.7 - - + -
144C VAL* 1.3 79.6 - - - +
146C THR* 1.3 64.7 + - - +
147C ILE* 3.5 32.1 - - + -
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Residues in contact with THR 146 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89C ALA 3.3 6.3 - - - -
90C PRO 4.7 0.9 - - - -
91C ALA* 3.2 26.7 - - - +
95C ALA* 5.0 4.3 - - - +
96C LYS* 5.1 12.4 - - + -
99C MET* 4.4 21.8 - - + -
100C PRO* 5.8 2.0 - - + -
110C VAL* 4.8 3.6 - - + -
111C LEU 2.9 10.2 + - - +
112C SER* 3.9 13.8 - - - +
113C ASP* 2.9 20.6 + - - -
114C VAL* 2.9 26.5 + - - +
145C PHE* 1.3 79.0 - - - +
147C ILE* 1.3 61.4 + - - +
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Residues in contact with ILE 147 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5C LEU* 5.9 0.2 - - + -
22C ALA* 4.5 19.3 - - + +
25C ALA* 3.7 10.8 - - + -
26C VAL* 5.2 3.6 - - + -
88C ALA* 4.5 8.3 - - + -
89C ALA 2.8 22.1 + - - +
90C PRO* 3.8 5.0 - - + +
91C ALA* 2.7 30.0 + - - +
114C VAL* 4.0 7.9 - - + +
117C ILE* 4.0 17.3 - - + -
145C PHE* 3.5 33.9 - - + -
146C THR* 1.3 73.1 - - - +
148C ARG* 1.3 65.1 + - - +
149C THR* 3.0 10.4 + - + +
152C PHE* 3.4 31.6 - - + -
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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