Contacts of the strand formed by residues 72 - 81 (chain C) in PDB entry 4BEI
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 72 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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39C VAL* 5.6 7.2 - - + -
40C ILE* 3.8 29.6 - - + -
66C ASN* 3.4 33.6 - - + +
68C SER* 5.4 4.0 - - - -
70C GLU 4.9 0.9 - - - +
71C THR* 1.3 74.8 + - - +
73C LYS* 1.3 71.9 + - - +
74C PHE* 3.9 4.5 - - + -
105C ALA* 3.3 5.3 - - - +
106C LEU* 2.9 41.0 + - + +
137C ALA* 4.7 10.1 - - + -
138C GLU* 5.3 2.7 - - + +
139C ASN* 6.3 1.8 - - - +
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Residues in contact with LYS 73 (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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71C THR 4.4 0.2 + - - -
72C VAL* 1.3 80.5 - - - +
74C PHE* 1.3 63.1 + - - +
103C SER* 4.2 18.8 - - - +
104C ASP 3.2 19.5 - - - +
105C ALA* 4.3 7.6 - - + +
138C GLU* 2.9 52.1 + - + +
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Residues in contact with PHE 74 (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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40C ILE* 4.0 14.4 - - + -
64C ILE* 3.9 25.1 - - + -
72C VAL* 3.9 6.7 - - + -
73C LYS* 1.3 80.1 - - - +
75C LYS* 1.3 67.3 + - - +
76C TYR* 3.7 23.3 - + - -
103C SER* 4.3 2.7 + - - -
104C ASP* 2.7 53.4 + - + +
105C ALA* 4.0 12.6 - - - -
106C LEU* 3.8 31.2 - - + -
112C LEU* 4.3 8.5 - - + -
135C VAL* 3.8 22.2 - - + -
136C VAL 3.4 12.8 - - - +
137C ALA* 3.8 10.5 - - + +
138C GLU 4.2 1.8 - - - +
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Residues in contact with LYS 75 (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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74C PHE* 1.3 73.9 - - - +
76C TYR* 1.3 60.6 + - - +
77C TRP* 4.0 14.0 - - + -
101C GLN* 2.8 30.7 + - + +
102C GLU* 3.9 12.3 - - - +
103C SER* 3.4 30.7 + - - +
135C VAL* 3.5 1.9 - - - +
136C VAL* 2.7 43.6 + - + +
237D ASN* 5.5 4.3 - - - +
239D ASP* 2.9 40.5 + - - -
241D SER* 4.8 3.8 - - - +
242D TYR* 3.9 26.7 - - + +
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Residues in contact with TYR 76 (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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62C LEU* 3.9 22.0 - - + -
64C ILE* 3.6 24.2 - - + -
74C PHE* 3.7 18.6 - + + -
75C LYS* 1.3 76.6 - - - +
77C TRP* 1.3 75.4 + - - +
101C GLN* 3.3 15.4 + - - -
102C GLU 4.8 3.4 + - - +
104C ASP* 3.7 23.4 + - + -
112C LEU* 4.0 16.4 - - + +
114C VAL* 3.7 22.8 - - + +
116C ARG* 4.0 18.8 + - - -
133C LEU* 3.9 9.4 - - + -
134C GLN 3.2 13.5 - - - +
135C VAL* 4.1 6.1 - - + -
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Residues in contact with TRP 77 (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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75C LYS* 4.0 17.0 - - + -
76C TYR* 1.3 96.2 - - - +
78C LEU* 1.3 61.0 + - - +
79C SER* 3.6 6.1 - - - -
101C GLN* 3.6 27.1 - - + +
116C ARG* 4.5 8.5 - - - +
132C SER 3.8 0.2 - - - +
133C LEU* 3.8 4.1 - - - +
134C GLN* 3.0 58.4 + - + +
136C VAL* 3.6 29.8 - - + -
212D LEU* 4.2 7.6 - - + -
213D ILE 3.2 9.7 + - - -
214D ILE* 3.5 24.2 - - + -
215D PRO* 3.4 33.2 - - + -
242D TYR* 3.7 31.4 - + - -
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Residues in contact with LEU 78 (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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44C LEU* 4.2 2.7 - - + -
60C SER* 3.8 21.1 - - - +
62C LEU* 4.1 20.0 - - + -
77C TRP* 1.3 77.0 - - - +
79C SER* 1.3 65.0 + - - +
89C PRO* 3.9 3.6 - - - +
90C ALA* 2.9 42.0 + - + +
91C LYS* 4.4 1.7 + - - +
116C ARG* 3.8 32.0 + - + +
117C GLY 6.1 0.2 - - - +
118C PHE* 4.4 13.5 - - + -
131C VAL* 3.8 15.3 - - + -
132C SER 3.6 14.8 - - - +
133C LEU* 3.7 23.1 - - + +
215D PRO* 4.5 2.6 - - - +
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Residues in contact with SER 79 (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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77C TRP* 3.6 8.6 - - - -
78C LEU* 1.3 77.0 + - - +
80C ILE* 1.3 65.4 + - - +
88C PHE 3.8 5.4 - - - -
89C PRO* 4.6 1.4 - - - +
90C ALA 4.2 0.4 - - - +
130C THR 3.9 0.5 - - - +
131C VAL* 3.6 1.6 - - - -
132C SER* 2.8 44.7 + - - -
134C GLN* 4.9 3.6 - - - -
205D THR* 5.7 0.2 - - - +
213D ILE* 2.6 51.1 + - - +
215D PRO* 3.6 8.8 - - - +
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Residues in contact with ILE 80 (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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79C SER* 1.3 82.5 - - - +
81C LYS* 1.3 63.9 + - - +
87C TYR* 3.5 4.3 - - - +
88C PHE* 2.8 86.7 + - + +
90C ALA* 4.2 14.1 - - + -
118C PHE* 3.8 18.2 - - + -
129C TYR* 3.8 18.2 - - + -
130C THR 3.5 7.0 - - - +
131C VAL* 3.6 29.2 - - + -
149C PHE* 4.2 11.0 - - + -
213D ILE* 4.6 5.4 - - - +
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Residues in contact with LYS 81 (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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80C ILE* 1.3 75.8 - - - +
82C GLY* 1.3 66.8 + - - +
86C ILE 3.5 11.0 - - - +
87C TYR* 3.6 29.4 - - + -
128C LYS 4.4 0.2 - - - +
129C TYR* 3.4 4.4 - - - -
130C THR* 2.7 49.2 + - - +
248C THR* 4.2 1.0 - - - +
1272C O4B 2.6 105.3 + - - +
213D ILE* 3.9 13.7 - - + -
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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