Contacts of the strand formed by residues 22 - 32 (chain D) 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 CYS 22 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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21D VAL* 1.3 74.0 - - - +
23D ARG* 1.3 72.7 + - - +
98D ARG* 3.5 11.2 - - - -
99D TYR 3.0 34.1 - - - +
100D ARG* 3.2 8.1 - - - -
101D GLU* 4.7 1.3 - - - +
139D THR* 3.4 5.0 - - - +
140D ARG* 2.8 29.8 + - - -
141D GLY 3.4 13.2 - - - +
142D CYS* 2.0 48.9 - - - -
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Residues in contact with ARG 23 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22D CYS* 1.3 77.2 - - - +
24D GLU* 1.3 62.5 + - - +
97D HIS 3.4 6.6 - - - +
99D TYR* 2.8 34.7 + - - +
101D GLU* 3.0 42.8 + - + +
133D VAL* 3.2 24.2 - - + -
134D ASN 3.4 10.4 + - - +
135D MET* 3.0 55.6 + - - +
137D ALA 3.6 10.2 + - - -
138D ARG 4.7 2.5 - - - +
139D THR* 3.3 30.3 - - + +
140D ARG* 3.5 13.7 - - - +
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Residues in contact with GLU 24 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23D ARG* 1.3 78.4 - - - +
25D ALA* 1.3 60.2 + - - +
26D SER* 4.8 4.0 + - - -
95D THR* 3.7 25.5 - - + +
96D ALA 3.4 6.7 - - - +
97D HIS* 4.3 12.4 + - - +
133D VAL* 3.5 3.8 - - - +
134D ASN* 2.6 69.1 + - + +
137D ALA* 4.9 4.2 - - + +
138D ARG 5.1 0.4 + - - -
140D ARG* 3.8 28.0 + - - +
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Residues in contact with ALA 25 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23D ARG 4.1 0.4 + - - -
24D GLU* 1.3 76.3 - - - +
26D SER* 1.3 63.2 + - - +
95D THR* 3.4 1.9 - - - +
96D ALA 2.8 34.4 + - - +
99D TYR* 3.5 45.3 - - + -
131D TRP* 3.9 5.8 - - + -
132D VAL 3.1 14.6 - - - +
133D VAL* 4.0 6.3 - - - -
134D ASN* 4.2 1.1 - - - +
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Residues in contact with SER 26 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24D GLU* 4.8 5.2 + - - -
25D ALA* 1.3 75.1 + - - +
27D ILE* 1.3 61.2 + - - +
28D SER* 5.6 0.4 - - - -
93D LYS* 3.6 26.3 - - - -
94D ILE 3.2 8.1 - - - -
95D THR* 3.1 24.1 + - - +
130D GLU 3.6 1.0 - - - +
131D TRP* 3.6 3.8 - - - -
132D VAL* 2.9 39.2 + - - +
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Residues in contact with ILE 27 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26D SER* 1.3 77.0 - - - +
28D SER* 1.3 70.1 + - - +
55D LEU* 3.7 15.7 - - + -
92D CYS 3.7 1.6 - - - +
93D LYS* 3.6 1.4 - - - -
94D ILE* 2.9 36.8 + - + +
111D PHE* 4.0 24.0 - - + -
119D PHE* 3.9 19.2 - - + -
129D PRO* 4.0 12.3 - - + -
130D GLU 3.6 29.2 - - - +
131D TRP* 3.5 40.4 - - + +
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Residues in contact with SER 28 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26D SER 5.6 0.3 - - - -
27D ILE* 1.3 76.3 - - - +
29D GLY* 1.3 58.4 + - - +
91D THR* 4.2 9.6 - - - +
92D CYS 3.3 7.2 - - - -
93D LYS* 3.6 25.1 - - - +
119D PHE* 3.8 3.6 - - - -
122D GLU* 3.4 23.2 - - - +
129D PRO* 3.2 26.9 - - - +
130D GLU 4.8 2.2 + - - +
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Residues in contact with GLY 29 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28D SER* 1.3 76.3 - - - +
30D GLU* 1.3 61.5 + - - -
91D THR* 3.6 3.2 - - - -
92D CYS* 2.8 34.5 + - - +
119D PHE* 3.1 24.4 - - - -
120D ARG 3.7 6.5 - - - -
122D GLU* 4.2 7.6 - - - -
129D PRO* 4.2 4.5 - - - -
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Residues in contact with GLU 30 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135A MET* 5.5 1.4 - - - +
29D GLY* 1.3 74.9 - - - -
31D ILE* 1.3 66.2 + - - +
32D ARG* 2.9 38.9 + - + +
89D LEU* 3.8 14.8 - - + +
90D CYS 3.4 11.0 - - - +
91D THR* 4.8 3.1 + - - +
118D ILE 4.2 0.7 - - - +
119D PHE* 3.1 6.8 - - - -
120D ARG* 2.6 49.9 + - - +
121D GLN 3.9 1.9 - - - +
122D GLU* 3.7 16.8 - - + +
123D THR* 2.8 47.9 + - - +
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Residues in contact with ILE 31 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30D GLU* 1.3 81.5 - - - +
32D ARG* 1.3 69.7 + - - +
33D TYR* 3.7 29.0 - - + +
44D ALA 5.6 0.7 - - - +
47D ASP* 4.5 4.7 - - + +
48D CYS* 4.5 12.6 - - + +
51D VAL* 4.4 5.2 - - + -
88D VAL 3.8 0.7 - - - +
89D LEU* 3.6 0.7 - - - -
90D CYS* 2.7 46.2 + - + +
92D CYS* 4.3 15.3 - - + -
118D ILE* 3.9 34.5 - - + +
119D PHE* 3.8 18.6 - - + -
120D ARG* 6.1 1.6 - - - +
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Residues in contact with ARG 32 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30D GLU* 2.9 35.9 + - - +
31D ILE* 1.3 80.1 - - - +
33D TYR* 1.3 73.7 + - - +
34D PRO* 4.6 0.9 - - - +
87D VAL* 3.9 12.3 - - + +
88D VAL 3.1 13.5 - - - +
89D LEU* 3.4 26.9 - - + +
120D ARG* 4.7 27.3 - - - +
121D GLN 4.6 7.9 + - - -
123D THR* 4.1 6.7 + - - -
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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