Contacts of the strand formed by residues 88 - 95 (chain D) in PDB entry 3T0E
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 SER 88 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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35D ARG* 5.2 0.4 - - - -
36D GLN 2.5 36.1 + - - -
37D PHE* 3.2 28.0 - - - +
38D PRO* 5.4 2.7 - - - -
86D ASP 3.1 2.6 + - - -
87D SER* 1.3 76.6 - - - +
89D PHE* 1.3 58.4 + - - +
90D TYR* 3.4 25.9 - - - -
109D THR 3.7 0.3 - - - +
110D ARG* 4.5 6.1 - - - +
111D LEU* 3.2 32.4 + - - +
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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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37C GLN* 4.1 0.9 - - - -
39C PRO 5.7 0.2 - - - -
40C SER* 3.8 16.8 - - - -
41C GLN* 3.7 41.5 - - - -
35D ARG* 3.3 2.1 - - - +
36D GLN* 2.5 67.7 + - + +
88D SER* 1.3 78.5 + - - +
90D TYR* 1.3 63.4 + - - +
91D ILE* 3.6 18.8 + - + +
107D ASN 4.0 4.3 - - - -
108D GLY* 3.6 29.8 - - - -
109D THR 4.0 9.0 - - - -
110D ARG* 4.3 20.4 - - + +
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Residues in contact with TYR 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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4D GLN* 3.0 8.7 + - - +
19D ILE* 4.4 22.4 - - + -
33D TRP* 5.7 2.9 - - + -
34D TYR 3.7 2.2 - - - +
35D ARG* 3.7 33.5 + - + -
45D MET* 3.9 29.2 - - + -
65D PHE* 4.1 14.9 - + - -
77D LEU* 4.2 15.0 - - + -
79D VAL* 5.0 9.0 - - + +
86D ASP* 3.2 23.2 + - - +
88D SER* 3.4 34.8 - - - -
89D PHE* 1.3 74.9 - - - +
91D ILE* 1.3 59.6 + - - +
109D THR 2.6 43.7 + - - +
111D LEU* 4.4 11.0 - - + -
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Residues in contact with ILE 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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37C GLN* 4.0 10.1 - - - +
42C GLY* 4.2 1.6 - - - -
43C PRO* 4.1 15.7 - - + -
4D GLN* 3.0 4.0 - - - +
32D PHE 4.0 0.2 - - - +
33D TRP* 3.8 3.1 - - - -
34D TYR* 2.6 53.0 + - + +
36D GLN* 4.1 2.5 - - + +
42D LEU* 3.6 24.2 - - + -
89D PHE* 3.6 41.7 - - + +
90D TYR* 1.3 76.8 - - - +
92D CYS* 1.3 68.7 + - - +
105D PHE* 4.1 20.0 - - + -
106D GLY 4.3 13.0 - - - +
108D GLY* 4.1 2.2 - - - -
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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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2D VAL* 4.3 2.7 - - - -
4D GLN* 2.1 37.9 + - - +
21D CYS* 2.0 53.6 - - - -
31D MET* 5.0 0.7 - - - -
32D PHE 3.5 5.6 - - - +
33D TRP* 3.5 31.2 - - + -
91D ILE* 1.3 69.8 - - - +
93D SER* 1.3 61.1 + - - +
105D PHE* 3.7 5.0 - - - -
106D GLY 3.3 22.7 + - - -
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Residues in contact with SER 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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2D VAL* 5.8 0.7 - - - -
31D MET* 3.4 12.8 - - - +
32D PHE* 2.9 58.1 + - - +
92D CYS* 1.3 78.1 - - - +
94D ALA* 1.3 60.1 + - - +
103D LEU* 3.9 14.1 - - - +
104D HIS 3.2 11.9 - - - -
105D PHE* 3.3 29.6 - - - -
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Residues in contact with ALA 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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2D VAL* 3.7 16.3 - - + +
23D SER* 4.7 2.5 - - - -
26D PHE* 3.6 28.5 - - + -
28D ALA* 4.1 12.8 - - + -
30D THR 3.7 4.9 - - - +
31D MET* 4.7 8.1 - - + -
32D PHE* 6.3 0.2 - - - -
93D SER* 1.3 74.3 - - - +
95D ARG* 1.3 62.5 + - - +
102D PRO 4.1 0.2 - - - +
103D LEU* 3.9 3.6 - - - +
104D HIS* 2.6 39.0 + - - +
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Residues in contact with ARG 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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61A ALA* 3.6 10.7 - - - +
90C TYR* 3.3 20.7 + - - -
95C ASN* 2.5 43.0 + - - +
26D PHE* 4.6 4.5 - - - -
28D ALA* 3.5 6.2 - - - -
29D THR 3.2 25.1 + - - -
30D THR* 3.2 26.1 + - - +
32D PHE* 3.2 28.8 - - + -
94D ALA* 1.3 72.6 - - - +
96D GLY* 1.3 57.6 + - - +
97D GLY 2.7 21.1 + - - +
98D SER* 3.0 32.5 + - - +
101D SER* 3.4 18.6 - - - +
102D PRO 3.9 3.4 - - - +
103D LEU* 3.4 23.8 - - + -
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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