Contacts of the strand formed by residues 21 - 32 (chain C) in PDB entry 4FPR
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 21 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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19C ALA 4.1 5.6 + - - +
20C TYR* 1.3 80.7 - - - +
22C CYS* 1.3 60.9 + - - +
23C ARG* 4.9 6.9 - - + +
101C GLU* 5.1 3.1 + - - +
102C PHE* 3.5 18.7 - - - -
139C THR* 3.7 35.4 - - + +
140C ARG 3.6 11.0 - - - +
141C GLY* 6.0 0.4 - - - -
142C CYS* 3.6 2.7 - - - -
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Residues in contact with CYS 22 (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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21C VAL* 1.3 73.6 - - - +
23C ARG* 1.3 70.5 + - - +
98C ARG* 3.5 22.0 - - - -
99C TYR 3.0 20.2 - - - +
100C ARG* 3.5 18.4 - - - +
101C GLU 5.3 0.2 - - - +
139C THR* 3.4 5.0 - - - -
140C ARG* 2.8 29.4 + - - -
141C GLY 3.7 11.9 - - - +
142C CYS* 2.0 48.4 - - - -
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Residues in contact with ARG 23 (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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21C VAL* 4.9 6.3 - - + +
22C CYS* 1.3 81.7 - - - +
24C GLU* 1.3 60.7 + - - +
97C HIS 3.5 3.5 - - - +
99C TYR* 3.0 34.9 + - + +
101C GLU* 4.0 27.5 - - + +
133C VAL* 3.8 25.9 - - + +
134C ASN 4.5 7.3 + - - +
135C MET* 3.2 49.8 + - - +
137C ALA 4.5 9.7 + - - +
138C ARG 5.0 0.2 - - - -
139C THR* 3.9 28.0 - - + +
140C ARG* 3.7 13.0 - - - +
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Residues in contact with GLU 24 (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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23C ARG* 1.3 74.7 - - - +
25C ALA* 1.3 65.9 + - - +
26C SER* 5.1 2.2 + - - +
95C THR* 3.7 26.7 - - + +
96C ALA 3.5 6.1 - - - +
97C HIS* 4.4 11.7 + - - +
133C VAL* 3.6 4.0 - - - +
134C ASN* 2.7 52.8 + - + +
137C ALA* 4.2 12.0 - - + +
140C ARG* 3.9 27.0 + - - +
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Residues in contact with ALA 25 (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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23C ARG 3.8 0.4 + - - -
24C GLU* 1.3 78.9 - - - +
26C SER* 1.3 60.1 + - - +
95C THR* 3.3 4.9 - - - +
96C ALA* 2.5 41.6 + - - +
99C TYR* 3.5 42.4 - - + -
131C TRP* 4.1 6.7 - - + -
132C VAL 3.2 13.0 - - - +
133C VAL* 4.0 6.7 - - + -
134C ASN* 4.4 1.1 - - - +
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Residues in contact with SER 26 (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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24C GLU* 5.1 2.6 + - - -
25C ALA* 1.3 71.8 + - - +
27C ILE* 1.3 61.1 + - - +
28C SER* 5.5 0.7 - - - -
93C LYS* 3.6 25.7 - - - -
94C ILE 3.1 6.5 + - - -
95C THR* 2.6 33.1 + - - +
130C GLU 3.4 1.4 - - - +
131C TRP* 3.4 4.6 - - - -
132C VAL* 2.7 45.5 + - - +
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Residues in contact with ILE 27 (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 SER* 1.3 75.6 - - - +
28C SER* 1.3 65.2 + - - +
55C LEU* 3.8 13.5 - - + -
92C CYS 3.9 0.5 - - - +
93C LYS* 3.5 1.8 - - - -
94C ILE* 2.9 37.4 + - + +
111C PHE* 3.8 33.4 - - + -
119C PHE* 4.2 12.7 - - + -
129C PRO* 4.1 12.3 - - + -
130C GLU* 3.4 24.9 - - - +
131C TRP* 3.5 52.7 - - + +
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Residues in contact with SER 28 (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 SER* 5.5 0.7 - - - -
27C ILE* 1.3 76.4 - - - +
29C GLY* 1.3 57.9 + - - +
91C THR* 4.6 6.3 - - - +
92C CYS 3.3 7.2 - - - -
93C LYS* 3.5 27.4 - - - +
119C PHE* 4.0 4.5 - - - -
122C GLU* 3.3 22.5 - - - +
129C PRO* 3.2 25.3 - - - +
130C GLU 4.4 2.8 + - - +
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Residues in contact with GLY 29 (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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28C SER* 1.3 76.0 - - - +
30C GLU* 1.3 60.6 + - - -
91C THR* 3.5 5.4 - - - +
92C CYS* 2.8 32.0 + - - -
119C PHE* 3.3 23.5 - - - -
120C ARG 3.6 9.9 - - - -
122C GLU* 3.9 8.7 + - - -
129C PRO* 4.3 1.8 - - - -
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Residues in contact with GLU 30 (chain C).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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135B MET* 5.4 2.1 - - - +
29C GLY* 1.3 74.5 - - - -
31C ILE* 1.3 66.9 + - - +
32C ARG* 3.2 30.5 + - - -
89C LEU* 3.4 21.3 - - + +
90C CYS 3.2 11.4 - - - +
91C THR* 4.7 3.5 + - - +
118C ILE 4.2 0.9 - - - +
119C PHE* 3.1 5.0 - - - -
120C ARG* 2.8 43.6 + - - +
121C GLN 3.8 2.5 - - - +
122C GLU* 3.7 16.0 - - + +
123C THR* 2.5 50.4 + - - +
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Residues in contact with ILE 31 (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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30C GLU* 1.3 79.5 - - - +
32C ARG* 1.3 69.2 - - - +
33C TYR* 3.7 30.2 - - + +
44C ALA 5.3 0.7 - - - +
47C ASP* 4.3 5.6 - - + +
48C CYS* 4.2 26.2 - - + +
51C VAL* 4.3 2.2 - - + -
88C VAL 3.9 1.0 - - - +
89C LEU* 3.7 0.7 - - - -
90C CYS* 2.8 40.7 + - + +
92C CYS* 4.4 8.5 - - + -
118C ILE* 4.0 34.3 - - + +
119C PHE* 3.7 21.3 - - + +
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Residues in contact with ARG 32 (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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30C GLU* 3.2 25.3 + - - +
31C ILE* 1.3 79.7 - - - +
33C TYR* 1.3 72.4 + - - +
34C PRO* 4.6 1.2 - - - +
87C VAL* 4.1 11.2 - - + -
88C VAL 3.5 2.5 - - - -
89C LEU* 3.1 28.1 - - + +
120C ARG* 3.7 47.0 - - - +
121C GLN 3.7 21.4 + - - -
123C THR* 4.5 5.1 + - - -
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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