Contacts of the helix formed by residues 90 - 104 (chain D) in PDB entry 5U03
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 90 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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41D PRO* 2.7 22.4 + - + +
42D TYR 2.6 25.3 + - - -
43D ILE* 3.3 14.1 - - + +
89D THR* 1.3 68.9 - - - +
91D GLY* 1.3 55.2 + - - +
93D ILE* 3.6 9.1 - - + +
94D TYR* 2.7 57.0 + - - +
155D GLU 4.3 6.3 - - - +
158D PRO* 6.4 0.9 - - + -
159D PHE* 3.8 33.2 - - + -
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Residues in contact with GLY 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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98B ILE* 4.1 9.2 - - - +
101B GLU* 5.1 0.7 - - - -
42D TYR 3.4 2.0 + - - -
43D ILE 2.9 26.2 + - - -
44D ASN 4.1 3.1 - - - -
45D ILE* 4.7 5.6 - - - -
89D THR* 3.2 3.4 + - - -
90D THR* 1.3 79.2 + - - +
92D LYS* 1.3 65.9 + - - +
94D TYR* 3.2 10.7 + - - +
95D GLN* 3.2 21.3 + - - +
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Residues in contact with LYS 92 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45D ILE* 3.6 28.3 - - + +
84D LYS* 5.4 4.2 - - - +
85D ASP* 5.7 5.2 + - - +
87D ASN 4.4 4.3 - - - +
88D LEU* 3.7 38.4 - - + -
89D THR* 3.1 24.1 + - + +
91D GLY* 1.3 77.9 - - - +
93D ILE* 1.4 65.2 + - + +
95D GLN* 3.2 4.3 + - - +
96D TYR* 3.0 21.6 + - + +
124D TRP* 3.7 26.0 - - + -
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Residues in contact with ILE 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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88D LEU* 5.3 10.8 - - + -
89D THR 3.0 18.5 + - - +
90D THR* 3.2 11.2 + - + +
92D LYS* 1.4 73.1 - - + +
94D TYR* 1.3 73.4 + - + +
96D TYR* 3.1 6.3 + - - +
97D VAL* 2.8 39.5 + - + +
117D ILE* 4.5 19.5 - - + -
120D ALA* 5.1 3.6 - - + -
121D ILE* 4.4 11.9 - - + -
124D TRP* 4.0 26.9 - - + +
159D PHE* 3.9 31.6 - - + -
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Residues in contact with TYR 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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94B TYR* 3.4 57.6 + + - -
98B ILE* 3.5 19.3 - - + -
43D ILE* 4.1 36.5 - - + +
90D THR* 2.7 38.3 + - - +
91D GLY* 3.5 11.2 - - - +
92D LYS 3.2 0.2 - - - -
93D ILE* 1.3 79.8 - - + +
95D GLN* 1.3 59.6 + - - +
97D VAL* 3.7 3.0 - - - +
98D ILE* 2.7 40.7 + - + +
117D ILE* 6.1 6.3 - - + -
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Residues in contact with GLN 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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95B GLN* 2.6 47.1 + - - +
98B ILE* 3.7 20.6 - - + +
45D ILE* 6.5 0.4 - - + -
91D GLY 3.2 9.0 + - - +
92D LYS* 3.9 6.5 - - - +
94D TYR* 1.3 78.6 - - - +
96D TYR* 1.3 63.7 + - - +
98D ILE* 3.7 7.0 - - - +
99D ASN* 2.8 60.8 + - - +
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Residues in contact with TYR 96 (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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92D LYS* 3.0 15.0 + - + +
93D ILE* 3.4 9.6 - - - +
95D GLN* 1.3 79.7 - - - +
97D VAL* 1.3 76.5 + - + +
99D ASN* 3.2 11.5 + - - +
100D LYS* 3.2 52.7 + - + +
106D TYR* 5.6 0.2 - - - -
120D ALA* 5.2 4.5 - - + -
123D GLU* 5.1 2.9 - - - -
124D TRP* 3.8 36.3 - + + -
127D ARG* 2.9 34.8 + - - -
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Residues in contact with VAL 97 (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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43B ILE* 5.1 1.3 - - + -
93D ILE* 2.8 37.6 + - + +
94D TYR* 3.8 3.4 - - - +
96D TYR* 1.3 81.9 - - + +
98D ILE* 1.3 55.5 + - + +
100D LYS* 2.8 8.9 + - - +
101D GLU* 2.7 55.7 + - + +
106D TYR* 4.4 15.5 - - + +
111D VAL* 4.2 7.2 - - + -
116D HIS* 5.9 0.9 - - + +
117D ILE* 3.9 25.1 - - + -
120D ALA* 4.6 11.0 - - + -
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Residues in contact with ILE 98 (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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43B ILE* 5.8 0.9 - - + -
45B ILE* 5.9 7.2 - - + -
91B GLY* 4.1 12.6 - - - +
94B TYR* 3.5 37.9 - - + -
95B GLN* 3.7 30.7 - - + +
98B ILE* 4.3 4.0 - - + -
94D TYR* 2.7 33.4 + - + +
95D GLN* 3.7 6.7 - - - +
97D VAL* 1.3 76.2 - - + +
99D ASN* 1.3 65.2 + - - +
101D GLU* 3.0 24.7 + - + +
102D ARG* 2.9 22.8 + - + +
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Residues in contact with ASN 99 (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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95D GLN* 2.8 54.6 + - - +
96D TYR* 3.4 11.9 - - - +
98D ILE* 1.3 77.6 - - - +
100D LYS* 1.3 59.0 + - + +
102D ARG* 3.0 9.6 + - - +
103D LYS* 2.9 44.6 + - - +
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Residues in contact with LYS 100 (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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96D TYR* 3.2 49.2 + - + +
97D VAL* 2.8 8.9 + - - +
99D ASN* 1.3 76.3 - - + +
101D GLU* 1.3 62.8 + - - +
103D LYS* 3.2 12.2 + - + +
104D GLY 3.1 3.6 + - - -
105D ASP* 2.8 63.6 + - - +
106D TYR* 3.2 35.2 - - + +
123D GLU* 5.9 2.5 - - - -
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Residues in contact with GLU 101 (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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43B ILE* 3.1 33.9 - - - +
44B ASN* 3.0 54.6 + - - +
45B ILE* 5.4 2.2 - - + +
49B THR* 5.8 2.6 - - - +
91B GLY* 5.1 0.3 - - - -
97D VAL* 2.7 26.1 + - + +
98D ILE* 3.0 23.4 + - + +
100D LYS* 1.3 78.1 - - - +
102D ARG* 1.3 59.0 + - - +
104D GLY* 2.9 20.1 + - - +
106D TYR* 4.1 15.9 - - + +
108D GLY* 5.1 4.0 - - - -
111D VAL* 3.1 12.0 - - + +
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Residues in contact with ARG 102 (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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44B ASN* 6.1 0.4 - - - -
45B ILE* 4.2 14.4 + - - +
46B ASP* 2.5 30.9 + - - +
49B THR* 3.4 31.3 - - - +
98D ILE* 2.9 13.2 + - + +
99D ASN* 3.0 11.4 + - - +
101D GLU* 1.3 76.8 + - - +
103D LYS* 1.3 61.6 + - + +
104D GLY* 3.0 2.1 + - - -
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Residues in contact with LYS 103 (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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99D ASN* 2.9 28.8 + - - +
100D LYS* 3.4 14.1 - - + +
101D GLU 3.1 0.2 - - - -
102D ARG* 1.3 76.4 - - + +
104D GLY* 1.4 59.4 + - - +
105D ASP* 3.3 30.8 + - - +
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Residues in contact with GLY 104 (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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101D GLU 2.9 17.4 + - - -
102D ARG 3.0 2.9 - - - -
103D LYS* 1.4 78.8 - - - +
105D ASP* 1.3 57.9 + - - +
106D TYR 3.0 6.7 - - - -
107D LEU* 2.9 21.8 + - - +
108D GLY* 4.2 13.7 - - - -
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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