Contacts of the helix formed by residues 107 - 116 (chain B) 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 SER 107 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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105B THR* 2.9 9.2 + - - -
106B TYR* 1.3 73.3 - - - +
108B CYS* 1.3 64.8 + - - +
109B TYR 3.2 0.6 + - - -
110B ARG* 3.6 6.8 + - - +
111B ILE* 2.8 32.6 + - - +
149B ASN* 4.5 0.2 + - - -
310B PHE* 5.3 9.8 - - - -
1336B HSA 2.8 31.2 + - - -
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Residues in contact with CYS 108 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230A PRO* 5.2 2.5 - - - -
106B TYR* 3.1 29.9 + - + +
107B SER* 1.3 84.7 + - - +
109B TYR* 1.3 58.3 + - - +
110B ARG 3.3 0.2 - - - -
111B ILE* 4.1 11.2 - - - -
112B PHE* 2.7 64.0 + - + -
1336B HSA 3.5 34.1 - - - -
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Residues in contact with TYR 109 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89B ILE* 3.6 36.8 - - + -
93B MET* 3.2 14.5 - - + +
101B PHE* 3.7 32.5 - + + -
105B THR* 3.3 29.6 - - + -
106B TYR* 3.0 37.8 + + + +
108B CYS* 1.3 77.4 - - - +
110B ARG* 1.3 58.5 + - - +
112B PHE* 5.0 0.9 - - - -
113B ALA* 3.0 25.6 + - - +
143B PHE* 3.6 33.4 - + + +
145B PRO* 3.5 16.1 - - + +
173B ASP* 3.2 31.2 + - - +
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Residues in contact with ARG 110 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12B TYR* 3.1 34.1 + - + -
101B PHE* 3.7 10.6 - - + -
103B PRO* 5.8 2.2 - - - +
106B TYR 4.5 0.2 + - - -
107B SER* 3.6 9.2 + - - +
108B CYS 3.3 0.2 - - - -
109B TYR* 1.3 76.4 - - - +
111B ILE* 1.3 67.9 + - + +
113B ALA* 3.2 3.1 + - - +
114B LYS* 2.9 45.1 + - + +
120B PHE* 4.4 10.5 - - + -
122B GLU* 2.8 45.5 + - - +
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Residues in contact with ILE 111 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226A ARG 5.3 4.9 - - - +
230A PRO* 6.0 2.0 - - + -
11B ALA* 5.4 1.5 - - + +
12B TYR* 4.0 51.2 + - + +
107B SER* 2.8 25.6 - - - +
108B CYS* 3.2 12.9 + - + +
110B ARG* 1.3 81.6 - - + +
112B PHE* 1.3 74.0 + - + +
114B LYS* 3.4 2.1 + - - +
115B ALA* 2.8 30.2 + - + +
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Residues in contact with PHE 112 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228A ARG 5.5 2.0 - - - -
229A LEU* 4.0 7.0 - - + -
230A PRO* 3.8 27.8 - - + -
86B ASP* 3.5 53.4 - - - -
89B ILE* 4.3 13.7 - - + -
90B TYR* 4.0 26.2 - + + -
93B MET* 3.9 15.7 - - + +
106B TYR* 5.2 0.4 - + - -
108B CYS* 2.7 47.9 + - + +
111B ILE* 1.3 86.3 - - + +
113B ALA* 1.3 62.8 + - - +
115B ALA* 3.4 6.5 - - + +
116B VAL* 2.9 28.2 + - - +
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Residues in contact with ALA 113 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93B MET* 3.6 20.1 - - + -
99B SER* 5.3 0.2 - - - -
101B PHE* 4.4 0.4 - - + -
109B TYR 3.0 19.9 + - - +
110B ARG 3.5 4.7 - - - +
112B PHE* 1.3 77.5 - - - +
114B LYS* 1.3 58.0 + - - +
117B GLY 3.0 6.1 + - - -
118B ALA* 2.8 39.3 + - + +
120B PHE* 3.5 33.9 - - + -
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Residues in contact with LYS 114 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9B LYS 5.3 2.0 + - - -
10B ARG* 3.3 47.3 + - - +
11B ALA* 4.4 5.7 - - - +
12B TYR* 3.5 34.9 + - + -
110B ARG* 2.9 30.2 + - + +
111B ILE* 3.9 3.1 - - - +
113B ALA* 1.3 73.7 - - - +
115B ALA* 1.3 66.3 + - - +
117B GLY* 3.0 12.0 + - - +
118B ALA 5.3 0.2 - - - -
120B PHE* 3.9 24.9 - - + -
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Residues in contact with ALA 115 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226A ARG 3.5 22.4 - - - +
227A VAL* 3.6 26.5 - - - +
228A ARG 5.6 0.7 - - - +
10B ARG* 2.5 28.8 + - - -
11B ALA* 4.0 12.7 - - + +
90B TYR* 4.9 2.0 - - + -
111B ILE* 2.8 22.2 + - + +
112B PHE* 3.2 11.0 + - + +
114B LYS* 1.3 77.1 - - - +
116B VAL* 1.3 54.3 + - + +
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Residues in contact with VAL 116 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94A LEU* 3.9 19.3 - - + +
10B ARG* 3.5 8.3 + - - +
90B TYR* 3.5 50.0 - - + +
93B MET* 5.2 4.3 - - + +
94B LEU* 2.9 33.4 - - + -
112B PHE* 2.9 16.1 + - + +
113B ALA 4.3 1.8 - - - +
115B ALA* 1.3 75.7 - - - +
117B GLY* 1.3 61.5 + - - +
118B ALA* 4.4 13.0 - - + +
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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