Contacts of the strand formed by residues 86 - 91 (chain D) in PDB entry 3UAJ
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 86 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37D TYR 4.0 0.3 - - - +
38D GLN* 3.7 2.3 - - - -
39D GLN* 2.8 46.9 + - - +
41D PRO* 5.9 1.6 - - - +
85D ALA* 1.3 71.1 - - - +
87D TYR* 1.3 62.7 + - - +
88D TYR* 3.6 33.4 - - + +
102D GLY* 4.4 2.2 - - - -
103D THR 3.4 22.9 - - - +
104D LYS* 3.8 24.1 - - + +
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Residues in contact with TYR 87 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7D GLN* 3.0 10.4 + - - -
22D ILE* 4.8 14.8 - - + -
36D TRP* 5.0 6.7 - + + -
37D TYR 3.3 15.5 - - - +
38D GLN* 3.0 26.6 + - + -
48D LEU* 3.6 26.9 - - + -
63D PHE* 3.5 14.9 - + - -
74D LEU* 4.4 12.3 - - + -
76D ILE* 3.7 16.8 - - + +
83D ASP 2.7 27.5 + - - -
85D ALA 3.3 26.2 - - - -
86D THR* 1.3 72.7 - - - +
88D TYR* 1.3 60.8 + - - +
102D GLY* 3.4 1.7 - - - -
103D THR* 2.8 42.2 + - - +
105D VAL* 3.7 24.0 - - + -
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Residues in contact with TYR 88 (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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39C GLN* 3.5 17.9 + - - -
44C GLY* 5.4 4.0 - - - -
45C LEU* 3.7 35.2 - - + -
7D GLN* 3.5 2.9 - - - -
35D ASN 4.0 0.3 - - - +
36D TRP* 3.5 8.6 - - - -
37D TYR* 2.8 47.0 + - + +
39D GLN* 3.4 31.1 + - + -
45D PRO* 5.7 0.2 - - + -
86D THR* 3.6 31.2 - - + +
87D TYR* 1.3 73.5 - - - +
89D CYS* 1.3 60.2 + - - +
99D PHE* 4.4 7.6 - + + -
100D GLY 3.9 14.6 - - - +
101D GLY 3.9 7.6 - - - -
102D GLY* 3.7 23.3 - - - -
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Residues in contact with CYS 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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5D MET* 4.8 2.2 - - - +
7D GLN* 3.2 26.2 + - - -
24D CYS* 2.0 53.3 - - + -
34D LEU* 4.2 4.9 - - + -
35D ASN 3.4 6.5 - - - +
36D TRP* 3.7 17.5 - - + -
88D TYR* 1.3 74.6 - - - +
90D GLN* 1.3 59.1 + - - +
98D THR 4.1 0.3 - - - +
99D PHE* 3.4 2.8 - - - -
100D GLY* 2.8 35.2 + - - -
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Residues in contact with GLN 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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108C ASP 3.3 12.7 + - - +
110C PHE* 3.4 20.9 - - - -
5D MET* 4.6 2.2 - - - -
34D LEU* 3.4 9.3 - - - +
35D ASN* 2.8 59.9 + - + +
37D TYR* 3.5 29.5 + - + -
88D TYR 4.4 0.2 - - - -
89D CYS* 1.3 74.5 - - - +
91D GLN* 1.3 88.1 + - - +
92D PHE* 4.2 2.0 - - - +
97D LEU* 4.4 8.1 - - - +
98D THR 3.4 13.0 - - - +
99D PHE* 3.7 23.3 - - + -
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Residues in contact with GLN 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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3D LEU* 3.5 18.8 - - + +
5D MET* 3.8 18.7 - - + +
30D ILE* 3.7 27.8 - - + +
33D ARG 4.0 4.7 - - - -
90D GLN* 1.3 87.6 + - - +
92D PHE* 1.3 60.8 + - - +
93D ASN* 3.5 2.4 + - - -
94D SER 2.9 33.0 + - - +
96D PRO 2.8 27.9 + - - -
97D LEU* 3.5 11.5 - - - +
98D THR* 3.1 33.8 + - - +
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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