Contacts of the helix formed by residues 141 - 146 (chain E) in PDB entry 1UW9
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 PRO 141 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33E ASP 3.3 25.6 - - - +
34E THR* 3.3 25.6 - - - +
35E ASP 3.6 9.9 - - - +
36E ILE* 3.7 22.2 - - + -
139E ARG* 3.3 17.0 - - - +
140E ILE* 1.3 85.5 - - - +
142E PRO* 1.3 71.6 - - + +
143E ALA 4.3 2.0 - - - +
144E TYR* 2.9 25.7 + - + +
145E VAL* 3.0 11.0 + - - +
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Residues in contact with PRO 142 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A THR* 4.3 14.8 - - + -
143A ALA* 4.3 1.1 - - + -
33E ASP 4.6 6.1 - - - +
139E ARG* 5.5 2.7 - - - +
140E ILE 3.8 3.3 - - - +
141E PRO* 1.3 84.6 - - + +
143E ALA* 1.3 56.0 + - - +
145E VAL* 3.6 10.0 - - + +
146E LYS* 2.9 36.7 + - - +
367E ASP* 3.8 39.3 - - + +
369E SMC 4.0 25.8 - - + -
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Residues in contact with ALA 143 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142A PRO* 4.3 4.0 - - + -
143A ALA* 3.7 32.0 - - + +
146A LYS* 3.4 25.9 - - + +
369A SMC 5.5 0.2 - - - -
33E ASP 5.6 0.2 + - - -
34E THR* 4.1 23.8 - - + -
105E ILE* 3.7 18.7 - - + +
141E PRO* 3.1 2.2 + - - +
142E PRO* 1.3 77.9 - - - +
144E TYR* 1.3 59.1 + - - +
146E LYS* 4.1 3.5 + - - +
147E THR* 3.6 5.9 - - - +
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Residues in contact with TYR 144 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146A LYS* 5.6 1.3 - - - -
36E ILE* 4.2 14.6 - - + -
105E ILE* 3.6 19.1 - - + +
108E PHE* 3.5 28.2 - + + +
109E GLU 2.8 32.4 + - - -
110E GLU* 4.2 2.5 - - + -
112E SER 3.4 15.6 + - - -
116E MET* 4.0 17.4 + - + +
140E ILE* 4.0 14.6 - - + -
141E PRO* 2.9 24.1 + - + +
143E ALA* 1.3 76.9 - - - +
145E VAL* 1.3 64.6 + - - +
146E LYS 3.1 1.8 - - - -
147E THR* 2.7 40.8 + - + -
148E PHE* 3.2 31.0 - + - -
320E MET* 4.0 6.5 - - + -
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Residues in contact with VAL 145 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140E ILE* 3.7 30.5 - - + +
141E PRO 3.0 17.7 + - - +
142E PRO* 3.6 9.4 - - + +
144E TYR* 1.3 75.3 - - - +
146E LYS* 1.3 60.1 + - + +
148E PHE* 3.1 33.5 + - - +
320E MET* 5.7 1.1 - - + -
367E ASP 4.0 12.1 - - - +
368E TRP* 3.4 36.6 - - + +
369E SMC 4.7 4.0 - - + +
371E MET* 3.7 27.4 - - + +
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Residues in contact with LYS 146 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105A ILE* 4.1 26.0 + - + +
106A ASP* 5.2 1.8 + - - -
108A PHE 5.2 1.4 + - - -
110A GLU* 3.0 46.3 + - - +
143A ALA* 3.4 30.5 - - + +
144A TYR* 5.6 1.3 - - - -
147A THR* 3.6 21.1 - - + +
210B PRO* 3.7 18.4 - - - +
142E PRO 2.9 20.9 + - - +
143E ALA 4.2 4.3 - - - +
144E TYR 3.1 0.4 - - - -
145E VAL* 1.3 79.4 - - + +
147E THR* 1.3 59.3 + - + +
148E PHE 3.2 6.7 + - - +
369E SMC 4.1 30.3 + - + +
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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