Contacts of the strand formed by residues 34 - 39 (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 LEU 34 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5D MET* 3.8 18.8 - - + -
24D CYS* 4.2 7.2 - - - -
30D ILE* 3.7 15.0 - - + -
32D ILE 3.3 4.0 + - - -
33D ARG* 1.4 72.5 - - - +
35D ASN* 1.3 70.8 + - - +
36D TRP* 3.4 40.3 - - + +
49D ILE 4.2 0.5 - - - +
50D TYR 3.8 0.5 - - - -
51D ASP 3.2 8.7 + - - -
52D ALA* 2.8 30.8 + - + -
72D PHE* 3.6 47.1 - - + -
89D CYS* 4.2 4.5 - - + -
90D GLN 3.4 11.4 - - - +
92D PHE* 3.3 4.7 - - - -
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Residues in contact with ASN 35 (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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106C SER* 4.5 0.3 + - - -
108C ASP 3.0 27.1 + - - -
109C SER* 3.5 15.8 - - - -
34D LEU* 1.3 81.8 - - - +
36D TRP* 1.3 63.5 + - - +
37D TYR* 3.8 10.7 - - + -
47D LEU* 3.8 7.0 - - + -
49D ILE 3.4 3.4 - - - -
50D TYR* 3.5 18.2 - - - +
51D ASP 3.5 0.9 + - - -
88D TYR 4.0 0.2 - - - +
89D CYS* 3.4 4.7 - - - -
90D GLN* 2.8 54.6 + - + +
92D PHE* 3.3 23.8 - - - -
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Residues in contact with TRP 36 (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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7D GLN* 4.3 7.0 - - - -
22D ILE* 3.8 28.3 - - + -
24D CYS* 3.6 32.5 - - + -
34D LEU* 3.4 22.1 - - + +
35D ASN* 1.3 72.2 - - - +
37D TYR* 1.3 61.4 + - - +
47D LEU* 3.4 8.7 - - - +
48D LEU* 3.0 28.4 + - + -
49D ILE* 2.7 40.7 + - + +
52D ALA* 4.7 6.9 + - - -
65D GLY* 5.2 0.7 - - - -
66D SER 5.0 0.4 + - - -
72D PHE* 4.5 2.4 - - + +
73D THR 4.0 18.5 + - - -
74D LEU* 3.6 54.1 - - + -
87D TYR* 5.0 6.7 - + + -
88D TYR 3.5 20.2 - - - -
89D CYS* 3.7 11.4 - - + -
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Residues in contact with TYR 37 (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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45C LEU* 5.8 0.4 - - + -
109C SER* 3.5 5.0 - - - -
110C PHE* 2.7 57.4 + + - -
113C TRP* 3.7 11.9 - + - -
35D ASN* 3.8 16.8 - - + -
36D TRP* 1.3 74.3 - - - +
38D GLN* 1.3 59.8 + - - +
45D PRO* 4.1 21.8 - - + -
46D LYS 3.4 6.3 - - - -
47D LEU* 3.6 29.3 - - + +
48D LEU* 4.3 4.5 - - - -
87D TYR* 3.3 11.6 - - - +
88D TYR* 2.8 48.3 + - + +
90D GLN* 3.5 27.8 + - + -
99D PHE* 4.1 16.4 - + + -
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Residues in contact with GLN 38 (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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37D TYR* 1.3 73.5 - - - +
39D GLN* 1.3 62.3 + - - +
40D LYS* 4.1 17.4 - - + +
44D ALA 4.3 0.9 - - - +
45D PRO* 3.4 1.4 - - - +
46D LYS* 2.7 56.8 + - + +
48D LEU* 3.6 23.5 - - + +
63D PHE* 3.6 20.0 - - - -
82D GLU 4.4 3.4 + - - +
83D ASP* 4.2 11.3 + - - +
85D ALA* 3.9 17.9 - - + -
86D THR 3.7 2.7 - - - -
87D TYR* 3.0 32.1 + - + -
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Residues in contact with GLN 39 (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* 2.8 43.8 + - - +
94C TYR* 3.6 12.5 + - - -
38D GLN* 1.3 75.3 - - - +
40D LYS* 1.3 61.6 + - - +
41D PRO* 4.6 0.7 - - - +
43D LYS 3.4 18.8 + - - +
44D ALA 4.8 0.9 - - - -
45D PRO* 3.5 36.9 - - + +
85D ALA* 3.8 4.4 - - - -
86D THR* 2.8 46.4 + - - +
88D TYR* 3.4 21.2 + - + -
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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