Contacts of the strand formed by residues 37 - 41 (chain D) in PDB entry 3UX9
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 37 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36D VAL* 1.3 76.3 - - - +
38D TRP* 1.3 63.7 + - - +
39D TYR* 3.7 14.8 - - - -
49D LEU* 4.2 0.4 - - - -
51D ILE 3.1 13.5 - - - -
52D TYR* 4.1 2.5 - - - -
53D ASP 5.1 0.6 + - - -
91D CYS* 3.3 3.6 - - - -
92D GLN* 2.8 44.4 + - - +
238D ASP 2.9 26.0 + - - -
239D HIS* 3.2 20.0 - - - +
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Residues in contact with TRP 38 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8D GLN* 3.9 14.8 - - - -
22D ILE* 3.4 26.0 - - + -
23D SER 4.3 1.6 - - - -
24D CYS* 3.6 30.5 - - + -
36D VAL* 3.9 12.6 - - + +
37D SER* 1.3 77.0 - - - +
39D TYR* 1.3 67.9 + - - +
49D LEU* 3.6 2.3 - - - +
50D LEU* 2.9 29.6 + - + -
51D ILE* 2.7 44.9 + - + +
54D ASN 4.9 4.8 + - - -
67D GLY* 5.0 0.8 - - - -
68D SER 5.3 0.6 + - - -
74D ALA* 4.0 6.0 - - + +
75D SER 3.8 10.9 + - - -
76D LEU* 3.5 52.5 - - + +
89D TYR* 4.8 1.6 - - + -
90D TYR 3.2 9.9 - - - -
91D CYS* 3.6 29.4 - - + -
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Residues in contact with TYR 39 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37D SER* 3.6 16.7 + - - -
38D TRP* 1.3 75.3 - - - +
40D GLN* 1.3 60.6 + - - +
47D PRO* 4.3 13.2 - - + -
48D LYS 3.5 3.6 - - - +
49D LEU* 3.7 21.5 - - + -
50D LEU* 4.5 3.4 - - - -
88D ASP 3.9 0.2 - - - +
89D TYR* 3.4 8.3 - - - +
90D TYR* 2.7 49.6 + - + +
92D GLN* 3.5 31.6 + - + -
103D PHE* 4.2 9.9 - + + -
179D LEU* 5.2 0.9 - - + -
239D HIS* 3.3 14.6 - - - +
240D MET* 3.0 52.1 + - + +
243D TRP* 3.9 25.8 - + + -
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Residues in contact with GLN 40 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39D TYR* 1.3 75.9 - - - +
41D GLN* 1.3 63.6 + - - +
42D LEU* 3.6 26.3 - - + +
46D ALA 4.3 0.2 - - - +
47D PRO* 3.2 2.8 - - - +
48D LYS* 2.7 61.8 + - + +
50D LEU* 3.9 23.9 - - + +
65D PHE* 4.3 14.3 - - - -
84D GLU 4.7 1.8 + - - -
85D ASP* 4.3 9.3 + - - +
87D ALA* 3.9 10.4 - - + +
88D ASP 3.7 2.7 - - - -
89D TYR* 2.9 37.2 + - + -
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Residues in contact with GLN 41 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40D GLN* 1.3 77.2 - - - +
42D LEU* 1.3 73.6 + - - +
43D PRO* 4.5 0.2 - - - +
44D GLY 5.7 0.7 - - - +
45D THR* 3.2 21.6 + - - +
47D PRO* 3.9 26.3 - - + +
87D ALA* 3.2 4.6 - - - +
88D ASP* 2.9 53.8 + - + +
90D TYR* 3.9 14.0 - - + -
173D GLN* 3.2 39.8 + - - +
179D LEU* 4.7 0.3 - - - +
229D TYR* 3.8 11.1 + - - -
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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
------------------------------------------------------------
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