Contacts of the helix formed by residues 106 - 117 (chain D) in PDB entry 1UU1
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 TYR 106 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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86D ASP* 2.7 25.4 + - - -
89D ILE* 3.9 7.4 - - + -
101D PHE* 5.5 0.2 - - - -
105D THR* 1.3 80.2 + - - +
107D SER* 1.3 69.4 + - - +
108D CYS* 3.1 29.0 - - + -
109D TYR* 3.1 59.2 + + + +
110D ARG* 4.3 1.7 + - - +
112D PHE* 4.9 1.3 - + - -
145D PRO* 4.5 0.8 - - + +
149D ASN* 3.4 26.3 + - + +
1335D PMP 3.6 45.7 - + + -
1336D HSA 3.2 43.8 + - - -
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Residues in contact with SER 107 (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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105D THR 3.0 7.9 + - - -
106D TYR* 1.3 73.0 - - - +
108D CYS* 1.3 64.9 + - - +
109D TYR 3.4 0.2 - - - -
110D ARG* 3.8 8.2 + - - +
111D ILE* 3.0 30.0 + - - +
310D PHE* 4.8 11.9 - - - -
1336D HSA 2.7 34.0 + - - -
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Residues in contact with CYS 108 (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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230C PRO* 5.2 4.3 - - - -
106D TYR* 3.1 39.8 - - + +
107D SER* 1.3 85.4 + - - +
109D TYR* 1.3 59.2 + - - +
110D ARG 3.1 1.8 - - - -
111D ILE* 3.5 14.4 - - - -
112D PHE* 2.8 56.9 + - + -
1336D HSA 3.8 21.5 - - - -
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Residues in contact with TYR 109 (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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89D ILE* 3.8 28.5 - - + -
93D MET* 2.9 26.4 - - + +
101D PHE* 3.5 34.7 - - + -
105D THR* 3.2 28.7 - - + -
106D TYR* 3.1 39.0 + + + +
108D CYS* 1.3 74.9 - - - +
110D ARG* 1.3 58.6 + - - +
112D PHE* 5.0 0.4 - - - -
113D ALA* 3.0 14.7 + - - +
143D PHE* 3.6 33.4 - + + +
145D PRO* 3.6 16.8 - - + +
173D ASP* 3.0 33.3 + - - +
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Residues in contact with ARG 110 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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12D TYR* 2.8 33.9 + - + +
101D PHE* 3.7 12.1 - - + -
106D TYR 4.3 0.9 + - - +
107D SER* 3.8 10.2 + - - +
109D TYR* 1.3 79.6 - - - +
111D ILE* 1.3 68.0 + - + +
113D ALA* 3.6 2.5 - - - +
114D LYS* 2.5 57.9 + - + +
120D PHE* 3.4 19.2 - - + -
122D GLU* 2.7 47.8 + - - +
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Residues in contact with ILE 111 (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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226C ARG 5.4 3.6 - - - +
230C PRO* 5.8 3.6 - - + -
12D TYR* 3.6 55.8 + - + +
107D SER* 3.0 26.5 - - - +
108D CYS* 3.2 19.7 + - - +
110D ARG* 1.3 82.1 - - + +
112D PHE* 1.3 73.4 + - + +
114D LYS* 3.8 1.7 + - - +
115D ALA* 3.1 28.1 + - + +
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Residues in contact with PHE 112 (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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228C ARG 5.3 2.0 - - - -
229C LEU* 3.7 11.7 - - + -
230C PRO* 3.6 26.9 - - + -
86D ASP* 3.6 51.8 - - + -
89D ILE* 3.9 20.6 - - + -
90D TYR* 4.0 22.9 - + + -
93D MET* 3.7 15.5 - - - -
106D TYR* 4.9 1.1 - + - -
108D CYS* 2.8 42.5 + - + +
111D ILE* 1.3 83.2 - - + +
113D ALA* 1.3 64.7 + - - +
115D ALA* 4.0 6.1 - - + -
116D VAL* 2.8 30.4 + - + +
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Residues in contact with ALA 113 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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93D MET* 3.5 14.8 - - + -
101D PHE* 4.1 0.7 - - + -
109D TYR 3.0 20.1 + - - +
110D ARG* 3.3 7.8 + - - +
112D PHE* 1.3 75.8 - - - +
114D LYS* 1.3 63.7 + - - +
117D GLY 3.0 2.8 + - - -
118D ALA* 2.9 37.9 + - + +
120D PHE* 3.7 34.8 - - + -
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Residues in contact with LYS 114 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10D ARG* 3.3 41.8 + - - +
11D ALA* 4.6 4.0 - - - -
12D TYR* 3.3 32.3 - - + -
110D ARG* 2.5 53.0 + - + +
111D ILE 4.2 2.0 - - - +
113D ALA* 1.3 77.5 - - - +
115D ALA* 1.3 58.5 + - - +
117D GLY* 2.8 20.5 + - - -
118D ALA 5.3 0.4 - - - -
120D PHE* 3.8 21.5 - - + -
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Residues in contact with ALA 115 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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94C LEU 5.5 0.5 - - - +
226C ARG 3.4 24.2 - - - +
227C VAL* 3.2 33.6 - - - +
228C ARG 5.6 0.2 - - - +
10D ARG* 3.6 13.0 + - - -
11D ALA* 4.2 15.4 - - + +
90D TYR* 5.3 1.1 - - + -
111D ILE* 3.1 22.5 + - + +
112D PHE* 3.6 9.6 - - + +
114D LYS* 1.3 78.8 - - - +
116D VAL* 1.3 59.2 + - + +
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Residues in contact with VAL 116 (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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94C LEU* 4.1 18.4 - - + +
227C VAL* 4.7 2.0 - - - -
10D ARG* 4.9 2.0 - - - -
90D TYR* 3.5 42.0 - - + +
93D MET* 4.4 11.0 - - + +
94D LEU* 3.5 38.0 - - + +
112D PHE* 2.8 18.2 + - + +
115D ALA* 1.3 73.7 - - - +
117D GLY* 1.3 59.9 + - - +
118D ALA* 3.7 24.0 - - + +
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Residues in contact with GLY 117 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10D ARG* 4.5 11.4 - - - +
113D ALA 3.0 0.6 + - - -
114D LYS* 2.8 17.7 + - - -
115D ALA 3.3 0.6 + - - -
116D VAL* 1.3 79.5 - - - +
118D ALA* 1.3 64.5 + - - +
119D LYS 3.8 0.9 + - - -
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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