Contacts of the strand formed by residues 88 - 97 (chain D) in PDB entry 1U1C
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 THR 88 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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20D THR* 3.0 9.2 + - - -
21D LEU* 3.9 30.0 - - + +
22D ALA 2.8 27.7 + - - -
86D ILE* 3.4 5.9 - - - +
87D ARG* 1.3 80.7 - - - +
89D PHE* 1.3 64.5 + - - +
90D LEU* 4.2 4.3 - - + -
136D CYS* 3.8 27.8 - - - -
212D ARG* 3.1 35.5 + - + +
252D LEU* 4.5 4.9 - - + -
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Residues in contact with PHE 89 (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 ALA* 3.4 3.4 - - + -
24D VAL* 4.1 17.0 - - + -
78D VAL* 3.4 48.5 - - + -
81D LEU* 3.7 30.7 - - + -
82D ALA* 4.2 2.0 - - + -
86D ILE* 3.5 37.9 - - + -
87D ARG 4.4 3.4 - - - -
88D THR* 1.3 75.5 - - - +
90D LEU* 1.3 62.4 + - - +
91D ARG 4.0 0.2 - - - -
202D LEU* 4.0 17.3 - - + +
206D CYS* 4.0 17.3 - - - -
211D LEU* 4.5 12.1 - - + -
212D ARG 2.9 13.6 + - - +
213D ALA* 3.2 3.9 - - + +
214D GLY 2.9 26.3 + - - +
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Residues in contact with LEU 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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21D LEU* 3.9 12.6 - - + -
22D ALA 2.9 12.2 + - - +
23D ILE* 3.4 10.6 - - + +
24D VAL* 2.9 24.7 + - - +
88D THR* 4.2 3.6 - - + -
89D PHE* 1.3 72.3 - - - +
91D ARG* 1.3 62.3 + - - +
92D ILE 3.7 0.7 + - - -
136D CYS* 4.1 7.2 - - + -
140D LEU* 4.0 30.3 - - + -
214D GLY* 3.7 11.9 - - - +
245D VAL* 3.9 18.7 - - + +
248D ALA* 4.3 2.0 - - + -
249D ALA* 3.8 38.8 - - + +
252D LEU* 3.8 26.7 - - + -
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Residues in contact with ARG 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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24D VAL* 3.3 21.3 + - + +
25D PRO 4.6 0.2 - - - -
26D GLY* 4.1 5.1 - - - +
67D THR* 4.7 3.5 + - + +
74D THR* 5.9 1.1 - - - -
89D PHE 3.9 1.6 + - - -
90D LEU* 1.3 72.0 - - - +
92D ILE* 1.3 62.8 + - - +
93D GLY* 3.5 12.8 - - - -
140D LEU* 5.5 0.5 - - - +
196D GLU* 2.8 29.5 + - - +
198D GLU* 2.8 42.8 + - - +
199D SER 4.3 2.7 - - - +
202D LEU* 3.7 23.6 - - + -
214D GLY 2.9 18.0 + - - +
215D MET* 3.1 29.5 - - - +
216D VAL* 3.0 32.4 + - - +
245D VAL* 4.3 1.5 - - - +
3032D PO4 3.0 33.1 + - - -
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Residues in contact with ILE 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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23D ILE* 3.8 27.6 - - + -
24D VAL 3.4 1.2 + - - -
25D PRO* 3.4 29.4 - - + +
30D ARG* 2.7 31.2 + - - +
34D ILE* 4.0 7.2 - - + -
91D ARG* 1.3 78.9 + - - +
93D GLY* 1.3 59.2 + - - +
216D VAL* 3.4 7.4 - - + -
238D GLU* 5.7 2.5 - - + -
241D ALA* 3.4 47.1 - - + +
242D VAL* 3.5 19.7 - - + +
245D VAL* 4.0 13.2 - - + -
3032D PO4 3.5 2.8 + - - -
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Residues in contact with GLY 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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30D ARG* 4.0 4.3 - - - -
91D ARG* 3.5 16.3 - - - +
92D ILE* 1.3 80.1 - - - +
94D THR* 1.3 64.3 + - - +
216D VAL 3.0 11.2 + - - -
217D ALA* 3.3 4.5 - - - -
218D GLY* 3.1 22.0 + - - -
241D ALA* 5.4 0.9 - - - +
3032D PO4 3.3 12.6 - - - -
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Residues in contact with THR 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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48C ARG* 4.0 7.2 + - - +
30D ARG* 4.0 9.2 - - - +
93D GLY* 1.3 77.6 - - - +
95D THR* 1.3 65.6 + - - +
196D GLU* 3.8 7.1 - - - +
217D ALA* 4.6 0.3 - - - +
218D GLY* 3.7 5.8 - - - +
220D ILE* 4.2 27.0 - - + +
238D GLU* 4.1 17.7 - - + +
3032D PO4 2.7 29.9 + - - +
5031D BAU 3.0 30.8 + - - -
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Residues in contact with THR 95 (chain D).
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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94D THR* 1.3 78.9 - - - +
96D GLY* 1.3 61.5 + - - +
108D LEU* 4.0 6.1 - - + -
194D ASN* 2.6 33.9 + - + +
195D TYR 2.7 18.6 + - - -
196D GLU* 4.6 1.6 - - - -
217D ALA* 3.8 15.0 - - + -
218D GLY 3.0 26.0 + - - +
219D VAL* 3.7 18.1 - - + -
220D ILE* 3.3 29.3 + - - +
221D VAL 3.8 1.4 + - - -
5031D BAU 3.7 9.2 - - - -
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Residues in contact with GLY 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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95D THR* 1.3 76.6 + - - +
97D ALA* 1.3 65.4 + - - -
98D ILE* 4.2 3.3 - - - +
194D ASN* 3.4 0.2 - - - -
195D TYR* 3.0 36.1 + - - +
221D VAL* 3.3 13.0 - - - -
223D ARG* 4.8 3.6 - - - -
5031D BAU 3.5 25.4 - - - -
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Residues in contact with ALA 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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95D THR* 4.0 2.4 + - - +
96D GLY* 1.3 74.5 - - - -
98D ILE* 1.3 59.4 + - - +
99D GLN 3.7 0.4 - - - +
102D ILE* 3.8 20.6 - - + -
193D MET 3.6 9.9 - - - +
194D ASN* 4.0 5.1 - - + +
219D VAL* 3.8 23.9 - - + +
221D VAL 2.8 8.8 + - - +
222D ASN* 3.4 20.2 - - - +
223D ARG* 2.8 29.5 + - - +
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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