Contacts of the strand formed by residues 89 - 100 (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 LEU 89 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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135A MET* 3.9 34.5 - - + +
136A LYS* 3.9 6.8 - - + +
30D GLU* 3.8 20.4 - - + +
31D ILE 3.7 3.4 - - - -
32D ARG* 3.4 29.2 - - + +
76D CYS* 3.5 1.2 - - - -
77D ALA* 2.9 35.8 + - + +
87D VAL* 3.6 21.7 + - + +
88D VAL* 1.3 72.9 - - - +
90D CYS* 1.3 62.4 + - - +
123D THR* 4.1 15.5 - - + +
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Residues in contact with CYS 90 (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* 3.4 6.7 - - - +
31D ILE* 2.7 49.3 + - + +
33D TYR* 3.8 25.1 - - + +
39D PRO* 4.9 0.7 - - - -
44D ALA* 4.2 2.9 - - + -
74D VAL* 4.0 10.8 - - + -
75D GLN 3.3 4.0 - - - +
76D CYS* 2.0 47.6 - - - -
88D VAL* 3.9 7.2 - - - -
89D LEU* 1.3 76.9 - - - +
91D THR* 1.3 63.1 + - - +
92D CYS* 3.7 1.2 + - + -
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Residues in contact with THR 91 (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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136A LYS* 2.7 34.2 + - - +
28D SER* 4.2 14.4 - - - +
29D GLY 3.6 8.7 - - - +
30D GLU* 4.8 4.0 + - - +
74D VAL* 3.2 8.4 - - - -
75D GLN* 2.8 35.7 + - - +
90D CYS* 1.3 72.4 - - - +
92D CYS* 1.3 63.4 + - - +
93D LYS* 3.8 5.0 + - + +
122D GLU* 3.9 28.0 + - - +
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Residues in contact with CYS 92 (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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27D ILE 3.7 2.1 - - - +
28D SER* 3.3 3.3 - - - -
29D GLY 2.8 37.8 + - - +
31D ILE* 4.3 13.9 - - + -
48D CYS* 2.1 62.1 - - + -
51D VAL* 3.9 10.3 - - - -
73D LYS 3.8 0.2 - - - -
74D VAL* 4.6 0.9 - - + -
90D CYS* 3.7 1.2 + - + +
91D THR* 1.3 72.9 - - - +
93D LYS* 1.3 56.6 + - - +
94D ILE* 3.1 24.8 - - - +
119D PHE* 3.9 5.1 - - + -
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Residues in contact with LYS 93 (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* 3.6 31.4 + - - -
27D ILE 3.6 4.5 - - - +
28D SER* 3.6 20.4 - - - +
71D THR 3.8 1.0 - - - +
72D ALA* 3.5 1.4 - - - -
73D LYS* 2.9 58.9 + - + +
91D THR* 3.8 6.5 + - + +
92D CYS* 1.3 71.9 - - - +
94D ILE* 1.3 64.4 + - - +
95D THR* 4.4 8.3 + - - +
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Residues in contact with ILE 94 (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* 3.2 3.3 - - - -
27D ILE 2.9 39.1 + - - +
48D CYS* 3.9 0.2 - - - -
51D VAL* 3.4 20.2 - - + -
52D THR* 3.7 23.8 - - - +
55D LEU* 4.0 20.0 - - + -
70D MET* 4.0 29.2 - - + -
71D THR 3.4 5.2 - - - +
72D ALA* 4.4 2.9 - - + -
92D CYS* 3.1 42.2 - - - +
93D LYS* 1.3 74.5 - - - +
95D THR* 1.3 64.0 + - - +
119D PHE* 4.2 4.9 - - + -
131D TRP* 3.9 3.9 - - + -
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Residues in contact with THR 95 (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* 3.7 23.6 - - + +
25D ALA 3.4 10.8 - - - +
26D SER* 3.1 14.1 + - - +
70D MET* 3.1 6.2 - - - -
71D THR* 2.8 44.9 + - - -
73D LYS* 5.5 7.1 + - - +
93D LYS* 4.4 10.6 + - - +
94D ILE* 1.3 73.5 - - - +
96D ALA* 1.3 60.5 + - - +
97D HIS* 3.4 26.8 - - + +
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Residues in contact with ALA 96 (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 0.7 - - - +
24D GLU* 3.4 4.5 - - - +
25D ALA 2.8 34.2 + - - +
66D TRP 3.5 23.3 - - - +
69D ASP 3.6 5.2 - - - -
70D MET* 3.8 8.5 - - + -
95D THR* 1.3 72.0 - - - +
97D HIS* 1.3 60.9 + - - +
98D ARG 3.6 0.8 + - - -
99D TYR* 4.2 12.6 - - + +
131D TRP* 3.6 29.0 - - + -
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Residues in contact with HIS 97 (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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41C LYS* 3.5 46.1 - - + +
23D ARG 3.4 5.0 - - - +
24D GLU* 4.3 11.1 + - - +
66D TRP 5.1 0.2 + - - -
69D ASP* 2.8 39.9 + - + +
71D THR* 2.6 31.4 + - + +
95D THR* 3.4 31.6 + - + +
96D ALA* 1.3 74.1 - - - +
98D ARG* 1.3 65.6 + - + +
140D ARG* 2.7 36.5 + - - +
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Residues in contact with ARG 98 (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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38C CYS* 5.6 2.0 - - - -
22D CYS* 3.5 14.5 - - - -
23D ARG 4.0 0.9 - - - -
64D ARG 4.7 0.9 - - - +
66D TRP 4.2 4.7 + - - -
67D GLY* 3.2 27.2 + - - -
68D ILE 5.6 0.4 - - - +
69D ASP* 4.4 19.0 + - + +
96D ALA 3.6 0.2 - - - -
97D HIS* 1.3 88.2 - - + +
99D TYR* 1.3 58.0 + - - +
100D ARG* 3.9 1.2 + - - -
140D ARG* 4.3 10.0 - - + +
141D GLY* 3.2 41.3 + - - +
142D CYS 4.0 13.8 - - - +
143D ASP 3.4 32.2 + - - -
144D HIS* 3.1 38.5 + - - +
145D HIS 5.1 0.4 - - - +
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Residues in contact with TYR 99 (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* 3.0 5.7 - - - +
23D ARG* 2.8 42.4 + - - +
25D ALA* 3.5 25.8 - - + -
65D ALA 3.9 2.7 - - - -
66D TRP* 3.2 43.4 + + + -
96D ALA* 4.2 14.4 - - + +
98D ARG* 1.3 69.8 - - - +
100D ARG* 1.3 82.1 + - - +
101D GLU* 3.3 5.0 + - + +
103D VAL 6.0 0.4 - - - -
105D LYS* 4.1 19.8 - - - +
106D ILE 5.3 0.2 + - - -
131D TRP* 3.2 38.2 - + + +
133D VAL* 3.8 23.8 - - + -
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Residues in contact with ARG 100 (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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21D VAL 4.2 0.4 - - - -
22D CYS* 3.5 8.4 - - - -
63D GLN* 2.9 23.6 + - - +
64D ARG* 2.9 36.9 + - - +
65D ALA* 3.1 25.7 + - - +
67D GLY* 4.6 4.8 - - - -
98D ARG 4.8 0.8 + - - -
99D TYR* 1.3 82.3 - - - +
101D GLU* 1.3 62.0 + - - +
102D PHE* 3.2 41.7 - - + -
103D VAL* 3.7 21.2 + - + +
142D CYS* 3.8 33.9 + - - +
143D ASP* 4.7 5.5 + - - -
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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