Contacts of the strand formed by residues 38 - 43 (chain D) in PDB entry 1WT5
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 38 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4D MET* 3.2 34.3 - - + -
23D CYS* 4.8 2.7 - - - -
29D ILE* 3.6 13.9 - - + -
36D THR* 2.8 18.1 + - + -
37D TYR* 1.3 72.5 - - - +
39D GLU* 1.3 61.1 + - - +
40D TRP* 4.3 16.2 - - + +
53D ILE 4.9 0.2 - - - -
54D TYR* 3.9 0.5 - - - -
55D LYS 3.5 5.0 + - - +
56D VAL* 3.0 43.4 + - + -
76D PHE* 3.1 43.7 - - + -
93D CYS* 4.9 0.7 - - + -
94D PHE 3.2 12.8 - - - +
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Residues in contact with GLU 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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102B PRO 4.1 3.6 - - - +
103B TYR* 3.3 13.0 - - - -
104B PHE* 2.9 32.0 + - - +
37D TYR* 4.5 7.4 - - - -
38D LEU* 1.3 82.7 - - - +
40D TRP* 1.3 64.0 + - - +
41D TYR* 2.6 37.1 + - + -
51D LEU* 4.1 2.0 - - + -
53D ILE 3.3 8.7 - - - +
54D TYR* 3.8 16.4 - - + -
55D LYS 4.5 1.5 + - - +
93D CYS* 3.2 4.3 - - - +
94D PHE* 2.5 66.6 + - + +
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Residues in contact with TRP 40 (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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6D GLN* 4.0 6.7 - - - -
21D ILE* 3.5 41.1 - - + -
23D CYS* 3.6 24.9 - - + -
38D LEU* 4.3 16.4 - - + +
39D GLU* 1.3 78.4 - - - +
41D TYR* 1.3 64.2 + - - +
51D LEU* 3.7 2.9 - - - +
52D LEU* 3.0 30.8 + - + -
53D ILE* 3.0 26.0 + - + +
56D VAL 4.9 8.7 + - - -
70D SER 5.7 0.4 + - - +
76D PHE* 4.3 1.5 - - + +
77D THR* 3.9 14.3 + - - +
78D LEU* 3.6 54.1 - - + +
91D TYR* 4.8 5.2 - - + -
92D TYR 3.3 20.9 - - - -
93D CYS* 3.6 23.6 - - + -
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Residues in contact with TYR 41 (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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45B LEU* 5.2 1.3 - - + -
104B PHE 4.1 0.2 + - - -
105B PHE* 3.1 47.4 + + + -
108B TRP* 4.3 11.4 - + - -
39D GLU* 2.6 38.8 + - + -
40D TRP* 1.3 76.6 - - - +
42D LEU* 1.3 60.1 + - - +
43D GLN 4.2 0.2 - - - -
49D PRO* 4.8 9.4 - - + -
50D GLN* 3.3 19.1 - - - +
51D LEU* 3.4 31.2 - - + +
52D LEU* 4.5 2.9 - - - +
90D VAL 3.9 0.5 - - - +
91D TYR* 3.3 4.5 - - - +
92D TYR* 2.7 50.6 + - + +
94D PHE* 3.7 27.8 - + + -
103D PHE* 4.3 9.9 - + + -
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Residues in contact with LEU 42 (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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41D TYR* 1.3 72.8 - - - +
43D GLN* 1.3 67.5 + - - +
44D LYS* 3.8 36.0 + - + +
48D SER 4.3 0.2 - - - +
49D PRO* 3.5 1.5 - - - +
50D GLN* 2.8 42.3 + - + +
52D LEU* 3.5 32.5 - - + +
67D PHE* 5.0 4.5 - - + -
87D ASP* 4.2 5.6 - - - +
88D VAL 4.3 0.4 - - - +
89D GLY* 4.0 16.8 - - - -
90D VAL 3.8 5.6 - - - +
91D TYR* 3.4 48.2 - - + +
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Residues in contact with GLN 43 (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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39B GLN* 3.1 30.4 + - - +
45B LEU* 3.7 17.0 - - - +
95B TYR* 2.9 25.3 + - - -
41D TYR 4.2 0.2 - - - -
42D LEU* 1.3 75.1 - - - +
44D LYS* 1.3 66.6 + - - +
46D GLY* 5.3 3.7 - - - +
47D GLN 2.8 27.4 + - - +
49D PRO* 4.0 22.5 - - + +
89D GLY* 3.6 1.2 - - - -
90D VAL* 3.1 48.3 + - + +
92D TYR* 4.6 4.0 + - + -
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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